James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-04-21 10:32:46

@James Fellows Yates has joined the channel

Emrah Kırdök (emrahkirdok@gmail.com)
2020-04-21 10:48:19

@Emrah Kırdök has joined the channel

Åshild (Ash) (ashild.v@gmail.com)
2020-04-21 11:59:25

@Åshild (Ash) has joined the channel

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-04-21 12:10:02

New preprint: https://www.biorxiv.org/content/10.1101/2020.04.20.050369v1.article-info

bioRxiv
An open-sourced bioinformatic pipeline for the processing of Next-Generation Sequencing derived nucleotide reads: Identification and authentication of ancient metagenomic DNA.
Bioinformatic pipelines optimised for the processing and assessment of metagenomic ancient DNA (aDNA) are needed for studies that do not make use of high yielding DNA capture techniques. These bioinformatic pipelines are traditionally optimised for broad aDNA purposes, are contingent on selection biases and are associated with high costs. Here we present a bioinformatic pipeline optimised for the identification and assessment of ancient metagenomic DNA without the use of expensive DNA capture techniques. Our pipeline actively conserves aDNA reads, allowing the application of a bioinformatic approach by identifying the shortest reads possible for analysis (22-28bp). The time required for processing is drastically reduced through the use of a 10% segmented non-redundant sequence file (229 hours to 53). Processing speed is improved through the optimisation of BLAST parameters (53 hours to 48). Additionally, the use of multi-alignment authentication in the identification of taxa increases overall confidence of metagenomic results. DNA yields are further increased through the use of an optimal MAPQ setting (MAPQ 25) and the optimisation of the duplicate removal process using multiple sequence identifiers (a 4.35-6.88% better retention). Moreover, characteristic aDNA damage patterns are used to bioinformatically assess ancient vs. modern DNA origin throughout pipeline development. Of additional value, this pipeline uses open-source technologies, which increases its accessibility to the scientific community. ### Competing Interest Statement The authors have declared no competing interest.
Original URL: https://www.biorxiv.org/content/10.1101/2020.04.20.050369v1.article-info
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-04-21 12:10:25

Does anyone know the authors and could ask for the supplement? It seems a lot of the information is there...

Åshild (Ash) (ashild.v@gmail.com)
2020-04-21 12:10:59

You could ask via twitter (?)

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-04-21 12:11:14

*Thread Reply:* WAs it originally tweeted by someone?

Åshild (Ash) (ashild.v@gmail.com)
2020-04-21 12:12:37

*Thread Reply:* Yep, first author tweeted it. His handle is at the bottom of the bioRxiv page for the paper

Becky Cribdon (r.cribdon@warwick.ac.uk)
2020-04-21 16:04:40

@Becky Cribdon has joined the channel

Becky Cribdon (r.cribdon@warwick.ac.uk)
2020-04-21 16:05:53

Could we do some shameless self-promotion with our latest paper? https://www.frontiersin.org/articles/10.3389/fevo.2020.00084/full

Frontiers
PIA: More Accurate Taxonomic Assignment of Metagenomic Data Demonstrated on sedaDNA From the North Sea
Assigning metagenomic reads to taxa presents significant challenges. Existing approaches address some issues, but are mostly limited to metabarcoding or optimized for microbial data. We present PIA (Phylogenetic Intersection Analysis): a taxonomic binner that works from standard BLAST output while mitigating key effects of incomplete databases. Benchmarking against MEGAN using sedaDNA suggests that, while PIA is less sensitive, it can be more accurate. We use known sequences to estimate the accuracy of PIA at up to 96% when the real organism is not represented in the database. For ancient DNA, where taxa of interest are frequently over-represented domesticates or absent, poorly-known organisms, more accurate assignment is critical, even at the expense of sensitivity. PIA offers an approach to objectively filter out false positive hits without the need to manually remove taxa and so make presuppositions about past environments and their palaeoecologies.
Original URL: https://www.frontiersin.org/articles/10.3389/fevo.2020.00084/full
:mask_parrot: James Fellows Yates, Åshild (Ash)
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-04-21 16:06:42

*Thread Reply:* Ofc ourse!

Sterling Wright (sterlingwright2016@utexas.edu)
2020-04-21 20:54:25

@Sterling Wright has joined the channel

Nico Rascovan (nicorasco@gmail.com)
2020-05-25 14:50:28

@Nico Rascovan has joined the channel

Maria Spyrou (spyrou@shh.mpg.de)
2020-05-25 19:24:49

@Maria Spyrou has joined the channel

Shreya (shreya23@uchicago.edu)
2020-05-25 21:15:41

@Shreya has joined the channel

Susanna Sabin (sjsabin@asu.edu)
2020-05-26 18:45:54

@Susanna Sabin has joined the channel

Maxime Borry (maxime.borry@gmail.com)
2020-05-28 14:56:27

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James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-06-08 09:27:41

https://www.nature.com/articles/s41467-020-16502-3

Nature Communications
Rapid range shifts and megafaunal extinctions associated with late Ple
The impact of late Pleistocene climate change on ecosystems has been hard to assess. Here, the authors sequence ancient DNA from Hall’s Cave, Texas and find that both plant and vertebrate diversity decreased with cooling, and though plant diversity recovered with rewarming, megafauna went extinct.
Original URL: https://www.nature.com/articles/s41467-020-16502-3
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-06-08 09:30:50

*Thread Reply:* Very honest too, props to htem!:

From the bulk bone samples, we did not find any evidence of cross contamination between samples, however, in one sample (HCB23_B) we identified significant contamination from fauna of New Zealand, which could stem from samples processed in the same laboratory for a different project. To identify the source of this contamination, we re-extracted and amplified the bone powder from HCB23_A and HCB23_B, which confirmed the presence of significant DNA contamination in the bone powder of both of these samples. Next, we returned to the original bulk bone samples, sampled and processed another 2x50 bones each. These samples contained only species from Texas and were comparable to other samples from the surrounding layers. Hence, we conclude that the bulk bone powder from the two subsamples of HCB23, was contaminated during the bone grinding stage. Most likely, this contamination stems from the reuse of a grinding pot that had not been cleaned properly. To confirm that this contamination event was a single incidence, we processed two ‘grinding blanks’ in which 15 mL of ultrapure water was run in the ball mill under the same configuration as the bulk bone samples. After grinding, the water sample was concentrated to 500 µL in an Amicon®Ultra-4 Centrifugal Filter (Millipore) and processed as a bulk bone sample. From these samples, we only identified background contamination from Homo sapiens

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-06-08 09:28:25

(I wonder how their data could be applied to PIA @Becky Cribdon? Looks like they take a similar-ish approach as they use BLAST)

Becky Cribdon (r.cribdon@warwick.ac.uk)
2020-06-08 09:44:26

Thanks for highlighting this, James. If they used BLAST, they should be able to use PIA. Looks interesting...

Becky Cribdon (r.cribdon@warwick.ac.uk)
2020-06-09 10:20:42

Hmm, they sequenced using metabarcoding. It would certainly be possible to analyse their data with PIA, but it's been developed for shotgun sequencing, so I'm not sure what effect it would have on the output. I've asked a friend who has done this sort of thing; it's a good question.

👍 James Fellows Yates
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-06-09 10:21:17

*Thread Reply:* Yeah, I realised that after too. Too used to sedaDNA being shotgun

Becky Cribdon (r.cribdon@warwick.ac.uk)
2020-06-11 09:37:23

*Thread Reply:* I'd like to see some more of it myself! Friend says PIA would probably do the same sort of thing on metabarcoding data, but it's not ideal.

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-06-11 09:37:59

*Thread Reply:* Did they say why it's not ideal? Not enough sequence diversity or somethin?

Åshild (Ash) (ashild.v@gmail.com)
2020-06-12 19:54:41

https://www.frontiersin.org/articles/10.3389/fevo.2020.00218/abstract

Frontiers
The challenges of reconstructing tropical biodiversity with sedimentary ancient DNA: a 2200-year-long metagenomic record from Bwindi Impenetrable Forest, Uganda
Sedimentary ancient DNA has been proposed as a key methodology for reconstructing biodiversity over time. Yet, despite the concentration of Earth’s biodiversity in the tropics, this method has rarely been applied in this region. Moreover, the taphonomy of sedimentary DNA, especially in tropical environments, is poorly understood. This study elucidates challenges and opportunities of sedimentary ancient DNA approaches for reconstructing tropical biodiversity. We present shotgun-sequenced metagenomic profiles and DNA degradation patterns from multiple sediment cores from Mubwindi Swamp, located in Bwindi Impenetrable Forest (Uganda), one of the most diverse forests in Africa. We describe the taxonomic composition of the sediments covering the past 2200 years and compare the sedimentary DNA data with a comprehensive set of environmental and sedimentological parameters to unravel the conditions of DNA degradation. Consistent with the preservation of authentic ancient DNA in tropical swamp sediments, DNA concentration and mean fragment length declined exponentially with age and depth, while terminal deamination increased with age. DNA preservation patterns cannot be explained by any environmental parameter alone, but age seems to be the primary driver of DNA degradation in the swamp. Besides degradation, the presence of living microbial communities in the sediment also affects DNA quantity. Critically, 92.3% of our metagenomic data of a total 81.8 million unique, merged reads c...
Original URL: https://www.frontiersin.org/articles/10.3389/fevo.2020.00218/abstract
👍 James Fellows Yates
Anneke ter Schure (a.t.m.t.schure@ibv.uio.no)
2020-06-18 10:27:55

@Anneke ter Schure has joined the channel

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-06-18 13:15:37

Not directly related to metagenomics methods per se, but for those working on oral microbiomes: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-020-06810-9 (via @ivelsko)

BMC Genomics
Analysis of oral microbiome from fossil human remains revealed the significant differences in virulence factors of modern and ancient Tannerella forsythia
Recent advances in the next-generation sequencing (NGS) allowed the metagenomic analyses of DNA from many different environments and sources, including thousands of years old skeletal remains. It has been shown that most of the DNA extracted from ancient samples is microbial. There are several reports demonstrating that the considerable fraction of extracted DNA belonged to the bacteria accompanying the studied individuals before their death. In this study we scanned 344 microbiomes from 1000- and 2000- year-old human teeth. The datasets originated from our previous studies on human ancient DNA (aDNA) and on microbial DNA accompanying human remains. We previously noticed that in many samples infection-related species have been identified, among them Tannerella forsythia, one of the most prevalent oral human pathogens. Samples containing sufficient amount of T. forsythia aDNA for a complete genome assembly were selected for thorough analyses. We confirmed that the T. forsythia-containing samples have higher amounts of the periodontitis-associated species than the control samples. Despites, other pathogens-derived aDNA was found in the tested samples it was too fragmented and damaged to allow any reasonable reconstruction of these bacteria genomes. The anthropological examination of ancient skulls from which the T. forsythia-containing samples were obtained revealed the pathogenic alveolar bone loss in tooth areas characteristic for advanced periodontitis. Finally, we analyzed the genetic material of ancient T. forsythia strains. As a result, we assembled four ancient T. forsythia genomes - one 2000- and three 1000- year-old. Their comparison with contemporary T. forsythia genomes revealed a lower genetic diversity within the four ancient strains than within contemporary strains. We also investigated the genes of T. forsythia virulence factors and found that several of them (KLIKK protease and bspA genes) differ significantly between ancient and modern bacteria. In summary, we showed that NGS screening of the ancient human microbiome is a valid approach for the identification of disease-associated microbes. Following this protocol, we provided a new set of information on the emergence, evolution and virulence factors of T. forsythia, the member of the oral dysbiotic microbiome.
Original URL: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-020-06810-9
👍 Åshild (Ash), Sterling Wright
ivelsko (velsko@shh.mpg.de)
2020-06-18 13:15:48

@ivelsko has joined the channel

ivelsko (velsko@shh.mpg.de)
2020-06-25 11:22:18

While we don’t have a session directly addressing data reporting, this is something worth working towards with ancient metagenomics https://www.biorxiv.org/content/10.1101/2020.06.24.167353v1.abstract?%3Fcollection=

bioRxiv
Strengthening The Organizing and Reporting of Microbiome Studies (STORMS)
Background: Human microbiome research is interdisciplinary, making concise organizing and reporting of results across the different styles of epidemiology, biology, bioinformatics, and statistics a challenge. Commonly used reporting guidelines for observational or genetic studies lack key aspects specific to microbiome studies. Methods: A multidisciplinary group of microbiome researchers reviewed elements of available reporting guidelines for observational and genetic studies, and adapted these for application to human microbiome studies. New reporting elements were developed for laboratory, bioinformatic, and statistical analysis specific to microbiome studies, and other parts of these checklists were streamlined to keep reporting manageable. Results: STORMS is a 18-item checklist for reporting on human microbiome studies, organized into six sections covering all sections of a scientific publication, presented as a table with space for author-provided details and intended for inclusion in supplementary materials. Conclusions: STORMS provides guidance for authors and standardization for interdisciplinary microbiome studies, facilitating complete and concise reporting. Availability: STORMS is downloadable as a versioned spreadsheet from <a href="http://storms.waldronlab.io">storms.waldronlab.io</a>. ### Competing Interest Statement The authors have declared no competing interest.
Original URL: https://www.biorxiv.org/content/10.1101/2020.06.24.167353v1.abstract?%3Fcollection=
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-07-11 07:28:37

https://www.frontiersin.org/articles/10.3389/fevo.2020.00218/full?utmsource=S-TWT&utmmedium=SNET&utmcampaign=ECOFEVOXXXXXXXXauto-dlvrit|https://www.frontiersin.org/articles/10.3389/fevo.2020.00218/full?utmsource=S-TWT&utmmedium=SNET&utmcampaign=ECOFEVOXXXXXXXXauto-dlvrit

Frontiers
The Challenges of Reconstructing Tropical Biodiversity With Sedimentary Ancient DNA: A 2200-Year-Long Metagenomic Record From Bwindi Impenetrable Forest, Uganda
Sedimentary ancient DNA has been proposed as a key methodology for reconstructing biodiversity over time. Yet, despite the concentration of Earth’s biodiversity in the tropics, this method has rarely been applied in this region. Moreover, the taphonomy of sedimentary DNA, especially in tropical environments, is poorly understood. This study elucidates challenges and opportunities of sedimentary ancient DNA approaches for reconstructing tropical biodiversity. We present shotgun-sequenced metagenomic profiles and DNA degradation patterns from multiple sediment cores from Mubwindi Swamp, located in Bwindi Impenetrable Forest (Uganda), one of the most diverse forests in Africa. We describe the taxonomic composition of the sediments covering the past 2200 years and compare the sedimentary DNA data with a comprehensive set of environmental and sedimentological parameters to unravel the conditions of DNA degradation. Consistent with the preservation of authentic ancient DNA in tropical swamp sediments, DNA concentration and mean fragment length declined exponentially with age and depth, while terminal deamination increased with age. DNA preservation patterns cannot be explained by any environmental parameter alone, but age seems to be the primary driver of DNA degradation in the swamp. Besides degradation, the presence of living microbial communities in the sediment also affects DNA quantity. Critically, 92.3% of our metagenomic data of a total 81.8 million unique, merged reads c...
Original URL: https://www.frontiersin.org/articles/10.3389/fevo.2020.00218/full?utm_source=S-TWT&amp;utm_medium=SNET&amp;utm_campaign=ECO_FEVO_XXXXXXXX_auto-dlvrit
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-07-22 21:22:53

https://www.nature.com/articles/s41586-020-2509-0.epdf?sharingtoken=Fokc0vGu-IVxAGM-Eoklf9RgN0jAjWel9jnR3ZoTv0NpPpYOltRo8eCU10MhBvEWhQqoi2QKPzxRSSOyHlQgjRgvcECA4D5qPQQVYNEsejo3Z3iCwS2P6-VcJ1mAydiBFXg1CIj5XcGzFv53H5ez5DwLKubtznja-lr7dWGYUDpHrvhDkKBz3tRNLYcpuXCpzbrZ-faUeyu8KXHaFUrqAG4v85AbDYW4xiG8XtvOd4jrev2LsdEFvutv13C&trackingreferrer=www.bbc.com|https://www.nature.com/articles/s41586-020-2509-0.epdf?sharingtoken=Fokc0vGu-IVxAGM-Eoklf9RgN0jAjWel9jnR3ZoTv0NpPpYOltRo8eCU10MhBvEWhQqoi2QKPzxRSSOyHlQgjRgvcECA4D5qPQQVYNEsejo3Z3iCwS2P6-VcJ1mAydiBFXg1CIj5XcGzFv53H5ez5DwLKubtznja-lr7dWGYUDpHrvhDkKBz3tRNLYcpuXCpzbrZ-faUeyu8KXHaFUrqAG4v85AbDYW4xiG8XtvOd4jrev2LsdEFvutv13C&trackingreferrer=www.bbc.com

nature.com
Evidence of human occupation in Mexico around the Last Glacial Maximum
Chiquihuite Cave (Zacatecas, Mexico) provides evidence of human presence in the Americas between about 33,000&amp;#8211;31,000 and 14,000&amp;#8211;12,000 years ago, and expands the cultural...
Original URL: https://www.nature.com/articles/s41586-020-2509-0.epdf?sharing_token=Fokc0vGu-IVxAGM-Eoklf9RgN0jAjWel9jnR3ZoTv0NpPpYOltRo8eCU10MhBvEWhQqoi2QKPzxRSSOyHlQgjRgvcECA4D5qPQQVYNEsejo3Z3iCwS2P6-VcJ1mAydiBF_Xg1CIj5XcGzF_v53H5ez5DwLKubtz_nja-lr7dWGYUDpHrvhDkKBz3tRNLYcpuXCp_zbrZ_-faUeyu8KXHaFUrqAG4v85AbDYW4xiG8XtvOd4jrev2LsdEFvutv13C&amp;tracking_referrer=www.bbc.com
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-07-22 21:23:23

Some sedaDNA in a really fascinating site it seems!

👍 Åshild (Ash)
Jessica Hider (hiderj@mcmaster.ca)
2020-07-28 19:42:48

@Jessica Hider has joined the channel

Abby Gancz (agancz@gmail.com)
2020-07-28 21:58:29

@Abby Gancz has joined the channel

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-08-11 08:30:46

☝️ maybe a good basis for SPAAM

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-08-11 08:31:06

STROBE-metagenomics: a STROBE extension statement to guide the reporting of metagenomics studies Summary The term metagenomics refers to the use of sequencing methods to simultaneously identify genomic material from all organisms present in a sample, with the advantage of greater taxonomic resolution than culture or other methods. Applications include pathogen detection and discovery, species characterisation, antimicrobial resistance detection, virulence profiling, and study of the microbiome and microecological factors affecting health. However, metagenomics involves complex and multistep processes and there are important technical and methodological challenges that require careful consideration to support valid inference. We co-ordinated a multidisciplinary, international expert group to establish reporting guidelines that address specimen processing, nucleic acid extraction, sequencing platforms, bioinformatics considerations, quality assurance, limits of detection, power and sample size, confirmatory testing, causality criteria, cost, and ethical issues. The guidance recognises that metagenomics research requires pragmatism and caution in interpretation, and that this field is rapidly evolving.

Pete Heintzman (peteheintzman@gmail.com)
2020-08-11 15:39:21

@Pete Heintzman has joined the channel

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-08-13 08:23:48

@Antonio Fernandez-Guerra has joined the channel

Maria Spyrou (spyrou@shh.mpg.de)
2020-08-31 14:07:50

New pathogen genomes: https://bmcbiol.biomedcentral.com/track/pdf/10.1186/s12915-020-00839-8

👍 James Fellows Yates
Ele (eg715@york.ac.uk)
2020-08-31 15:20:35

@Ele has joined the channel

ivelsko (velsko@shh.mpg.de)
2020-09-01 10:13:54

“The archives are half-empty: an assessment of the availability of microbial community sequencing data” https://www.nature.com/articles/s42003-020-01204-9

Communications Biology
The archives are half-empty: an assessment of the availability of microbial community sequencing data
Jurburg et al. explored the discrepancies between reported and actual availability of archived 16S rRNA sequencing data in the microbial literature. They identify that only a small portion of archived datasets can be reliably accessed and used by researchers.
Original URL: https://www.nature.com/articles/s42003-020-01204-9
Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-01 10:18:45

This is a sad reality…

Pooja Swali (swalipooja@gmail.com)
2020-09-01 12:28:01

@Pooja Swali has joined the channel

Pete Heintzman (peteheintzman@gmail.com)
2020-09-02 11:34:35

“Optimizing extraction and targeted capture of ancient environmental DNA for reconstructing past environments using the PalaeoChip Arctic-1.0 bait-set” https://www.cambridge.org/core/journals/quaternary-research/article/optimizing-extraction-and-targeted-capture-of-ancient-environmental-dna-for-reconstructing-past-environments-using-the-palaeochip-arctic10-baitset/BDC98B87B7A68968FA99204512D8ECFE

Cambridge Core
Optimizing extraction and targeted capture of ancient environmental DNA for reconstructing past environments using the PalaeoChip Arctic-1.0 bait-set | Quaternary Research | Cambridge Core
Optimizing extraction and targeted capture of ancient environmental DNA for reconstructing past environments using the PalaeoChip Arctic-1.0 bait-set - Tyler J. Murchie, Melanie Kuch, Ana T. Duggan, Marissa L. Ledger, Kévin Roche, Jennifer Klunk, Emil Karpinski, Dirk Hackenberger, Tara Sadoway, Ross MacPhee, Duane Froese, Hendrik Poinar
Original URL: https://www.cambridge.org/core/journals/quaternary-research/article/optimizing-extraction-and-targeted-capture-of-ancient-environmental-dna-for-reconstructing-past-environments-using-the-palaeochip-arctic10-baitset/BDC98B87B7A68968FA99204512D8ECFE
👍 James Fellows Yates, Becky Cribdon
😀 Jessica Hider
Pete Heintzman (peteheintzman@gmail.com)
2020-09-02 11:35:33

*Thread Reply:* Could not see any raw data released, unfortunately - but a great paper for those working with ancient environmental DNA!

aidanva (aida.andrades@gmail.com)
2020-09-03 09:57:32

@aidanva has joined the channel

Valentina Zaro (valentina.zaro@unifi.it)
2020-09-03 10:51:41

@Valentina Zaro has joined the channel

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-07 16:27:08

And another!

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-07 16:27:09

Saidi-Mehrabad, A., Neuberger, P., Cavaco, M. et al. Optimization of subsampling, decontamination, and DNA extraction of difficult peat and silt permafrost samples. Sci Rep 10, 14295 (2020). https://doi.org/10.1038/s41598-020-71234-0

👍 Pete Heintzman
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-07 16:27:17

I guess sedaDNA is all the range atm ;

🎉 Pete Heintzman
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-07 16:27:19

😉

Becky Cribdon (r.cribdon@warwick.ac.uk)
2020-09-11 11:38:45

Woop woop!

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-11 12:16:37

https://www.annualreviews.org/doi/abs/10.1146/annurev-micro-012520-072314?af=R

👍 Åshild (Ash), aidanva, Sterling Wright
Nico Rascovan (nicorasco@gmail.com)
2020-09-21 15:40:06

https://pubmed.ncbi.nlm.nih.gov/32943086/

PubMed
Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graph - PubMed
Our findings demonstrate that aligning aDNA sequences to variation graphs effectively mitigates the impact of reference bias when analyzing aDNA, while retaining mapping sensitivity and allowing detection of variation, in particular indel variation, that was previously missed.
Original URL: https://pubmed.ncbi.nlm.nih.gov/32943086/
Nico Rascovan (nicorasco@gmail.com)
2020-09-21 15:40:28

This is a nice method from few days ago

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-09-21 15:40:47

*Thread Reply:* Poop-gen only though 😢

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-10-02 21:49:23

Ancient viruses from Japanese teeth? https://www.nature.com/articles/s10038-020-00841-6

Journal of Human Genetics
Identification of ancient viruses from metagenomic data of the Jomon people
Ancient DNA studies provide genomic information about the origins, population structures, and physical characteristics of ancient humans that cannot be solely examined by archeological studies. The DNAs extracted from ancient human bones, teeth, or tissues are often contaminated with coexisting bacterial and viral genomes that contain DNA from ancient microbes infecting those of ancient humans. Information on ancient viral genomes is useful in making inferences about the viral evolution. Here, we have utilized metagenomic sequencing data from the dental pulp of five Jomon individuals, who lived on the Japanese archipelago more than 3000 years ago; this is to detect ancient viral genomes. We conducted de novo assembly of the non-human reads where we have obtained 277,387 contigs that were longer than 1000 bp. These contigs were subjected to homology searches against a collection of modern viral genome sequences. We were able to detect eleven putative ancient viral genomes. Among them, we reconstructed the complete sequence of the Siphovirus contig89 (CT89) viral genome. The Jomon CT89-like sequence was determined to contain 59 open reading frames, among which five genes known to encode phage proteins were under strong purifying selection. The host of CT89 was predicted to be Schaalia meyeri, a bacterium residing in the human oral cavity. Finally, the CT89 phylogenetic tree showed two clusters, from both of which the Jomon sequence was separated. Our results suggest that metagenomic information from the dental pulp of the Jomon people is essential in retrieving ancient viral genomes used to examine their evolution.
Original URL: https://www.nature.com/articles/s10038-020-00841-6
👀 Anna F.
Zandra Fagernäs (fagernaes@shh.mpg.de)
2020-10-05 10:37:37

Multi-omic detection of Mycobacterium leprae in archaeological human dental calculus: https://royalsocietypublishing.org/doi/pdf/10.1098/rstb.2019.0584

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-10-05 10:43:37
👍 Lucy van Dorp, Katerina Guschanski
ivelsko (velsko@shh.mpg.de)
2020-10-05 15:39:55

*Thread Reply:* all the paywalled articles:

05_RSTB20190583.pdf
❤️ Becky Cribdon
😀 Jessica Hider
ivelsko (velsko@shh.mpg.de)
2020-10-05 15:40:13

*Thread Reply:*

06_RSTB20190580.pdf
ivelsko (velsko@shh.mpg.de)
2020-10-05 15:40:26

*Thread Reply:*

07_RSTB20190578.pdf
ivelsko (velsko@shh.mpg.de)
2020-10-05 15:40:36

*Thread Reply:*

10_RSTB20190577.pdf
ivelsko (velsko@shh.mpg.de)
2020-10-05 15:40:45

*Thread Reply:*

11_RSTB20190576.pdf
ivelsko (velsko@shh.mpg.de)
2020-10-05 15:40:53

*Thread Reply:*

12_RSTB20190570.pdf
ivelsko (velsko@shh.mpg.de)
2020-10-14 14:52:52

*Thread Reply:* @Zandra Fagernäs here

Pete Heintzman (peteheintzman@gmail.com)
2020-10-29 21:31:05

Cool paper, but no raw data released unfortuntely: "Denisovan DNA in Late Pleistocene sediments from Baishiya Karst Cave on the Tibetan Plateau" https://science.sciencemag.org/content/370/6516/584

Science
Denisovan DNA in Late Pleistocene sediments from Baishiya Karst Cave on the Tibetan Plateau
Two archaic lineages overlapped with modern humans outside of Africa: the well-studied Neanderthals and their more mysterious cousins, the Denisovans. Denisovan remains are rare, being limited to Denisovan Cave in Siberia and a putative, undated jaw from Tibet. However, there is evidence for multiple introgressions from Denisovans into modern-day humans, especially in Australasian populations. By examining the sediment of Baishiya Karst Cave located on a high plateau in Tibet, Zhang et al. identified ancient mitochondrial DNA from Denisovans indicating their presence at about 100 thousand, 60 thousand, and possibly 45 thousand years ago. This finding provides insight into the timing and distribution of Denisovans in Asia and extends the time of occupation of the Tibetan plateau by hominins. Science , this issue p. [584][1] A late Middle Pleistocene mandible from Baishiya Karst Cave (BKC) on the Tibetan Plateau has been inferred to be from a Denisovan, an Asian hominin related to Neanderthals, on the basis of an amino acid substitution in its collagen. Here we describe the stratigraphy, chronology, and mitochondrial DNA extracted from the sediments in BKC. We recover Denisovan mitochondrial DNA from sediments deposited ~100 thousand and ~60 thousand years ago (ka) and possibly as recently as ~45 ka. The long-term occupation of BKC by Denisovans suggests that they may have adapted to life at high altitudes and may have contributed such adaptations to modern humans on the Tibetan Plateau. [1]: /lookup/doi/10.1126/science.abb6320
Original URL: https://science.sciencemag.org/content/370/6516/584
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-10-29 21:31:22

*Thread Reply:* No?

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-10-29 21:31:25

*Thread Reply:* Or still embargoed?

Pete Heintzman (peteheintzman@gmail.com)
2020-10-29 21:33:07

*Thread Reply:* Only human mito consensus sequences released. No mention of raw data:

"Data and materials availability: ... The new mitochondrial consensus files reported in this paper have been deposited in the Genome Warehouse in National Genomics Data Center (24), Beijing Institute of Genomics (China National Center for Bioinformation), Chinese Academy of Sciences, under accession number PRJCA002765, which is publicly accessible at https://bigd.big.ac.cn/gwh...."

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-10-29 21:39:15

*Thread Reply:* FFS

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-10-29 21:39:40

*Thread Reply:* Poop-gen 😏 .

👏 Sterling Wright, Becky Cribdon
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-11-07 15:26:25

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7585846/

PubMed Central (PMC)
Two Nearly Complete Nosocomial Pathogen Genome Sequences Reconstructed from Early-Middle 20th-Century Dental Calculus
Acinetobacter baumannii and Stenotrophomonas maltophilia genomes were reconstructed from early-middle 20th-century human skeletal remains, maintained in natural history museums, using a metagenomic binning approach.
Original URL: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7585846/
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-11-07 15:28:29

De novi assembly and binning of C20 bacterial genomes from dental calculus

Anna F. (annakfos@gmail.com)
2020-11-13 16:07:21

https://www.nature.com/articles/s41559-020-01351-6

Nature Ecology &amp; Evolution
Researchers using environmental DNA must engage ethically with Indigenous communities
The study of environmental DNA can reveal information about the history and presence of Indigenous communities on their lands — potentially even inadvertently. Better engagement with the ethical aspects of environmental DNA research is required in the field as a whole, and especially for researchers working on Indigenous lands.
Original URL: https://www.nature.com/articles/s41559-020-01351-6
👍 Anneke ter Schure, Abby Gancz, Pete Heintzman, Raphael Eisenhofer
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-11-20 09:13:12

https://www.biorxiv.org/content/10.1101/2020.11.14.382994v4

bioRxiv
Challenges in Benchmarking Metagenomic Profilers
Accurate microbial identification and abundance estimation are crucial for metagenomics analysis. Various methods for classifying metagenomic data and estimating taxonomic profiles, broadly referred to as metagenomic profilers, have been developed. Yet, benchmarking metagenomic profilers remains challenging because some tools are designed to report relative sequence abundance while others report relative taxonomic abundance. Here, we show how misleading conclusions can be drawn by neglecting this distinction between relative abundance types when benchmarking metagenomic profilers. Moreover, we show compelling evidence that interchanging sequence abundance and taxonomic abundance will influence both per-sample summary statistics and cross-sample comparisons. We suggest that the microbiome research community should pay attention to potentially misleading biological conclusions arising from this issue when benchmarking metagenomic profilers, by carefully considering the type of abundance data that was analyzed and interpreted, and clearly stating the strategy used for metagenomic profiling. ### Competing Interest Statement The authors have declared no competing interest.
Original URL: https://www.biorxiv.org/content/10.1101/2020.11.14.382994v4
👍:skin_tone_3: Anna F.
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-11-20 09:13:42

". We find that microbiome data analysis based on sequence abundance will underestimate (or overestimate) the relative abundances of microbes with smaller (or larger) genome sizes. This will fundamentally affect differential abundance analyses and other analytical methods that rely on accurate counts in their input contingency matrix"

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-11-20 09:15:12

"Taken together, these analyses emphasize the importance of differentiating between relative sequence abundance and relative taxonomic abundance in metagenomic profiling. Ignoring this distinction can potentially underestimate the relative abundance of organisms with small genome sizes."

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-11-20 09:19:50

Some more formalised pangenome graphs for on-humans!

https://www.biorxiv.org/content/10.1101/2020.11.12.380378v2

bioRxiv
Nucleotide-resolution bacterial pan-genomics with reference graphs
Bacterial genomes follow a U-shaped frequency distribution whereby most genomic loci are either rare (accessory) or common (core) - the alignable fraction of two genomes from a single species might be only 50%. Standard tools therefore analyse mutations only in the core genome, ignoring accessory mutations. We present a novel pan-genome graph structure and algorithms implemented in the software pandora , which approximates a sequenced genome as a recombinant of reference genomes, detects novel variation and then pan-genotypes multiple samples. Constructing a reference graph from 578 E. coli genomes, we analyse a diverse set of 20 E. coli isolates. We show, for rare variants, pandora recovers at least 13k more SNPs than single-reference based tools, achieving equal or better error rates with Nanopore as with Illumina data, and providing a stable framework for analysing diverse samples without reference bias. This is a significant step towards comprehensive analyses of bacterial genetic variation. ### Competing Interest Statement The authors have declared no competing interest.
Original URL: https://www.biorxiv.org/content/10.1101/2020.11.12.380378v2
Katerina Guschanski (katerina.guschanski@ebc.uu.se)
2020-11-23 17:26:20

Why are the authors silent on this paper? It's a great read! https://www.sciencedirect.com/science/article/pii/S1040618220307746

sciencedirect.com
Do I have something in my teeth? The trouble with genetic analyses of diet from archaeological dental calculus
Dental calculus and other preserved microbiome substrates are an attractive target for dietary reconstruction in past populations through a variety of…
Original URL: https://www.sciencedirect.com/science/article/pii/S1040618220307746
:partyparrot: Anna F.
🎉 Anna F.
🤩 Ele
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-11-23 17:27:27

*Thread Reply:* Because they didn't tell us as first they uploaded an uncorrected version... and it's meant to be OA but they won't reply to us about how we can pay for it 🤦 .

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-11-23 17:27:46

*Thread Reply:* But I see the final version is live, so will tweet it in a bit 😅

Katerina Guschanski (katerina.guschanski@ebc.uu.se)
2020-11-23 17:28:15

*Thread Reply:* Congratulations! Just reading the intro now (and checked out the figures) and I love it!

❤️ James Fellows Yates
Katerina Guschanski (katerina.guschanski@ebc.uu.se)
2020-11-23 17:27:09

https://www.biorxiv.org/content/10.1101/2020.09.28.316869v1

bioRxiv
Simulation of bacterial populations with SLiM
Simulation of genomic data is one of the key tool in population genetics, yet, to date, there is no forward-in-time simulator of bacterial populations that is both computationally efficient and adaptable to a wide range of scenarios. Here we demonstrate how to simulate bacterial populations with SLiM, a forward-in-time simulator built for eukaryotes. SLiM gained lots of traction in the past years, and has exhaustive documentation showcasing the various scenarios that are possible to simulate. This paper focuses on a simple demographic scenario, to explore bacterial specificities and how it translates into SLiM’s language. To foster the development of bacterial simulations with this recipe, we pedagogically walk the reader through the code. We also validate the simulator, by testing extensively the results of the simulations against existing simulators and theoretical expectations of some summary statistics. Finally, the combination of this protocol with the flexibility and power of SLiM enables the community to simulate efficiently bacterial populations under a wide range of evolutionary scenarios. ### Competing Interest Statement The authors have declared no competing interest.
Original URL: https://www.biorxiv.org/content/10.1101/2020.09.28.316869v1
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-12-07 14:05:39

Series of responses to ancient small pox (issues of applying modern assemblies to ancient DNA) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7716422/

PubMed Central (PMC)
Response to Brinkmann et al. “Re-assembly of 19th century smallpox vaccine genomes reveals the contemporaneous use of horsepox and horsepox-related viruses in the United States”
We thank Brinkmann and colleagues for their correspondence and their further investigation into these American Civil War Era vaccination strains. Here, we summarize the difficulties and caveats of work with ancient DNA.
Original URL: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7716422/
👍 Åshild (Ash), Sterling Wright
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-12-07 21:26:50

If anyone is curious how Archaeogenetics at MPI-SHH samples teeth for pathogen DNA, we just made our sampling protocol in step-by-step format open access and citable on protocols.io! https://dx.doi.org/10.17504/protocols.io.bqebmtan (Co written with SPAAM members @Gunnar Neumann and @aidanva!)

protocols.io
Tooth Sampling from the inner pulp chamber for ancient DNA Extraction
This protocol describes how to obtain powder from the inner pulp chamber of teeth for the extraction of ancient DNA. It is ideal for the simultaneous isolation of both host endogenous...
Original URL: https://dx.doi.org/10.17504/protocols.io.bqebmtan
🤩 Kelly Blevins
👏 Katerina Guschanski
Gunnar Neumann (gunnar_neumann@eva.mpg.de)
2020-12-07 21:26:56

@Gunnar Neumann has joined the channel

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-12-20 19:48:48

https://www.biorxiv.org/content/10.1101/2020.12.16.419085v1

Katerina Guschanski (katerina.guschanski@ebc.uu.se)
2020-12-23 15:20:47

Some group and self-promotion. All and any comments welcome! https://www.biorxiv.org/content/10.1101/2020.12.22.423960v1

bioRxiv
Wild animal oral microbiomes reflect the history of human antibiotics use
Following the advent of industrial-scale antibiotics production in the 1940s, antimicrobial resistance (AMR) has been on the rise and now poses a major global health threat. Because AMR can be exchanged between humans, livestock and wildlife, evaluating the potential of wild animals to act as AMR reservoirs is essential. We used shotgun metagenomics sequencing of dental calculus, the calcified form of the oral microbial biofilm, to determine the abundance and repertoire of AMR genes in the oral microbiome of Swedish brown bears from museum specimens collected over the last 200 years. Our temporal metagenomics approach allowed us to establish a baseline of natural AMR in the pre-antibiotics era and to quantify a significant increase in total AMR load and diversity of AMR genes that is correlated with human antibiotics use. We also demonstrated that Swedish public health policies were effective in limiting AMR spillover into wildlife. ### Competing Interest Statement The authors have declared no competing interest.
Original URL: https://www.biorxiv.org/content/10.1101/2020.12.22.423960v1
:mask_parrot: James Fellows Yates, Pooja Swali, Zandra Fagernäs
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2020-12-23 15:21:20

*Thread Reply:* Woohoo! Finally! Excited to read it!

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-01-04 21:29:51

Comparison of lab decontamination procedures of dental calculus

https://www.researchsquare.com/article/rs-136836/v1

Research Square
Effectiveness of Decontamination protocols when Analyzing Ancient DNA Preserved in Dental Calculus
Ancient DNA analysis of human oral microbial communities within calcified dental plaque (calculus) has revealed key insights into human health, paleodemography, and cultural behaviors. However, contamination imposes a major concern for paleomicrobiological samples due to their low endogenous D...
Original URL: https://www.researchsquare.com/article/rs-136836/v1
👍 Katerina Guschanski
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-01-04 21:37:14

Coauthored by @Sterling Wright !

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-01-04 21:41:05

*Thread Reply:* Small suggestion @Sterling Wright you may want to rename your GitHub repo (if not too late), 'decontam' is the same name as a (very good!) R package: https://github.com/benjjneb/decontam

Which has a statistical method for predicting likely lab contaminations.

benjjneb/decontam
<p>Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data</p>
Website
<p><a href="https://benjjneb.github.io/decontam/">https://benjjneb.github.io/decontam/</a></p>
Stars
<p>83</p>
<a href="https://github.com/benjjneb/decontam">benjjneb/decontam</a>
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-01-04 21:41:14

*Thread Reply:* You might not want people to get confused, and I've seen some fights over bioinformatic tool names.... (Look up falcon ancient DNA metagenomics)

Sterling Wright (sterlingwright2016@utexas.edu)
2021-01-05 03:38:03

*Thread Reply:* Thank you for the heads up James! I’ll make sure to get with the co-authors and change it ASAP

👍 James Fellows Yates
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-01-13 13:07:24

Something similar what we would like to do for metagenomics but for c14 dating!

https://royalsocietypublishing.org/doi/10.1098/rsos.201351

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-01-21 19:13:04

https://twitter.com/AmineNamouchi/status/1352230217776037888?s=19

Maybe something interesting to replace MultiVCFAnalyzer? Has anyone had any experience with this?

twitter
} {name: Amine, surname: Namouchi} (https://twitter.com/AmineNamouchi/status/1352230217776037888)
If you want to: - Explore, Filter, Annotate, and Combine your <b>#SNPs</b> and <b>#indels</b> from VCF files. - Visualize and Analyze your samples using two dimension reduction techniques: <b>#PCA</b> and #UMAP Check #snpToolkit, a tool I am developing. <https://snptoolkit.readthedocs.io/en/latest/index.html> <https://pbs.twimg.com/media/EsQVvujXcAAG59t.jpg>
Original URL: https://twitter.com/AmineNamouchi/status/1352230217776037888?s=19
Twitter
👀 Kelly Blevins
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-01-27 07:31:07

In case anyone isn't in Twitter, the first paper coming spinning out of the SPAAM community is now out! https://twitter.com/ScientificData/status/1354059031883747330?s=19

twitter
} Scientific Data (https://twitter.com/ScientificData/status/1354059031883747330)
Ancient <b>#DNA</b> &amp; <b>#RNA</b> are valuable data sources for a wide range of disciplines. Here are Community-#curated &amp; standardised <b>#metadata</b> of published ancient <b>#metagenomic</b> samples with AncientMetagenomeDir, presented by <a href="https://twitter.com/jfy133">@jfy133</a> et al of <a href="https://twitter.com/MPI_SHH">@MPI_SHH</a>. <https://go.nature.com/3iZclmp>
Original URL: https://twitter.com/ScientificData/status/1354059031883747330?s=19
Twitter
:partyparrot: Anna F., Shreya
🎉 Anna F., Katerina Guschanski, Shreya
🤸‍♀️:skin_tone_3: Anna F.
🥳 Gunnar Neumann
👏 Betsy Nelson
Ele (eg715@york.ac.uk)
2021-02-04 19:29:46

New dog poop paper: https://www.nature.com/articles/s41598-021-82362-6#Sec11

Scientific Reports
Integrative analysis of DNA, macroscopic remains and stable isotopes of dog coprolites to reconstruct community diet
Paleofeces or coprolites are often used to reconstruct diet at archaeological sites, usually using macroscopic analyses or targeted DNA amplification and sequencing. Here we present an integrative analysis of dog coprolites, combining macroscopic analyses, stable isotope measurements, and DNA shotgun sequencing to examine diet and health status. Dog coprolites used in this study were recovered from the Janey B. Goode and East Saint Louis archaeological sites, both of which are located in the American Bottom, an extensive Mississippi River floodplain in Southwestern Illinois. Based on the context of recovery, coprolites are assigned to the Late Woodland and Terminal Late Woodland periods (ca. 600–1050 AD). Given the scarcity of human remains from this time period, these dog coprolites can be useful as a proxy for understanding human diet during the Late Woodland period. We find that the Late Woodland dogs consumed a variety of fish as well as bird and plant taxa, possibly including maize, and also harbored intestinal parasites and pathogenic bacteria. By sequencing the fecal microbiome of the coprolites, we find some similarities to modern dog microbiomes, as well as specific taxa that can be used to discriminate between modern and ancient microbiomes, excluding soil contaminants. As dogs are often used as a surrogate to assess human diet, humans living with these dogs likely had a similar diet and were affected by similar parasites. These analyses, when integrated, show a more comprehensive view of ancient dog and human diet and health in the region during the initial expansion of maize agriculture than any individual method could alone.
Original URL: https://www.nature.com/articles/s41598-021-82362-6#Sec11
:thumbsup_all: Katerina Guschanski, James Fellows Yates
💩 Anna F.
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-02-04 21:06:29

*Thread Reply:* @Ele could you add the paper as an issue to the 'Dir

Although I hope they've uploaded the raw data and didn't remove the <75bp as they do in the analysis :/

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-02-05 15:02:26

*Thread Reply:* Just added it as I had a spare moment and so we don't forget!

Abby Gancz (agancz@gmail.com)
2021-02-04 19:42:26

oooh nice

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-02-11 17:14:13

a primer on aDNA including the first citation for AncientMetagenomeDir!!! Written by PIs of a lot of aDNA labs from around the world! Free pdf link courtesy of @Christina Warinner!

https://rdcu.be/ce8Bp

https://rdcu.be/ce8Bp

👍 Anneke ter Schure
:partyparrot: Shreya, aidanva
🎉 Shreya, Katerina Guschanski, Pooja Swali
Åshild (Ash) (ashild.v@gmail.com)
2021-02-11 17:17:14

Can you share a PDF? Can’t download from that link

Christina Warinner (warinner@shh.mpg.de)
2021-02-11 17:17:42

@Christina Warinner has joined the channel

ivelsko (velsko@shh.mpg.de)
2021-02-11 17:17:52
Primer_s43586-020-00011-0_1613044666_1.pdf
:thumbsup_all: Katerina Guschanski, Åshild (Ash), Gunnar Neumann, Sterling Wright, Betsy Nelson, Emrah Kırdök
👀 Raphael Eisenhofer
👍 Betsy Nelson, Abby Gancz
ivelsko (velsko@shh.mpg.de)
2021-02-16 08:46:03

Hi All, does anyone have access to this and could share the pdf? “How reliably do metagenome-assembled genomes (MAGs) represent natural populations? Insights from comparing MAGs against isolate genomes derived from the same fecal sample” https://aem.asm.org/content/early/2021/01/12/AEM.02593-20

ivelsko (velsko@shh.mpg.de)
2021-02-16 08:57:26

*Thread Reply:* Awesome, thanks!

Katerina Guschanski (katerina.guschanski@ebc.uu.se)
2021-02-16 08:57:50

*Thread Reply:* 😁

ivelsko (velsko@shh.mpg.de)
2021-02-25 13:18:15

“Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative’s Workshop and Follow-On Activities” https://msystems.asm.org/content/6/1/e01194-20

👍 James Fellows Yates
🙌:skin_tone_3: Anna F.
👍:skin_tone_4: Miriam Bravo
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-02-25 13:21:45

*Thread Reply:* Pet peeve: 'national intiative for xyz'... national for WHO!?

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-02-25 13:22:00

*Thread Reply:* It sucks for LIMS too 'Natural History Museum' x1000000

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-02-25 13:23:45

*Thread Reply:* (vi) Establish a certification of “compliance.” Despite the significant efforts already invested in defining minimum standards for microbiome data, such as the Minimum Information about any (x) Sequence (MIxS) packages (39), important work remains to ensure that the various standards and ontologies are interoperable and easily accessible to the research community. This entails working with researchers to identify metadata attributes that are valuable for data reuse within their respective communities, and defining community-specific benchmarks. Establishing a “certification of compliance” based on these benchmarks would enable designation of data sets ready for reuse, which encourages inclusion in follow-up studies and enhances their citation metrics (see section i above).

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-02-25 13:23:40

@Antonio Fernandez-Guerra ☝️

ivelsko (velsko@shh.mpg.de)
2021-03-15 16:07:56

One for the calculus people: “Resilience of the oral microbiome” https://doi.org/10.1111/prd.12365 … “Diet, with the exception of excessive and/or frequent consumption of fermentable carbohydrate or supplementation with nitrate, has minimal impact on the composition of the oral bacterial community.“. This is quite a different perspective compared to stool studies

👍 Abby Gancz, Zandra Fagernäs, James Fellows Yates, aidanva, Sterling Wright, Katerina Guschanski
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-03-16 14:11:35

nf-core/eager paper is out!

Fellows Yates JA, Lamnidis TC, Borry M, Andrades Valtueña A, Fagernäs Z, Clayton S, Garcia MU, Neukamm J, Peltzer A. 2021. Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager. PeerJ 9:e10947 https://doi.org/10.7717/peerj.10947

Any suggestions for improving the metagenomic component welcome! Development doesn't stop here 🚀

PeerJ
Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager
The broadening utilisation of ancient DNA to address archaeological, palaeontological, and biological questions is resulting in a rising diversity in the size of laboratories and scale of analyses being performed. In the context of this heterogeneous landscape, we present an advanced, and entirely redesigned and extended version of the EAGER pipeline for the analysis of ancient genomic data. This Nextflow pipeline aims to address three main themes: accessibility and adaptability to different computing configurations, reproducibility to ensure robust analytical standards, and updating the pipeline to the latest routine ancient genomic practices. The new version of EAGER has been developed within the nf-core initiative to ensure high-quality software development and maintenance support; contributing to a long-term life-cycle for the pipeline. nf-core/eager will assist in ensuring that a wider range of ancient DNA analyses can be applied by a diverse range of research groups and fields.
Original URL: https://doi.org/10.7717/peerj.10947
:thumbsup_all: Katerina Guschanski, Sterling Wright
🎉 ivelsko, Anna F., Pooja Swali, Ele, Nikolay Oskolkov
👏:skin_tone_2: Kelly Blevins
🙌:skin_tone_4: Miriam Bravo
👏 Becky Cribdon
Becky Cribdon (r.cribdon@warwick.ac.uk)
2021-04-20 16:49:44

*Thread Reply:* Ahh, I've been trying and failing to use EAGER - this could be the answer to all of my problems!! Very excited to try this, and congratulations on publication.

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-04-20 16:53:33

*Thread Reply:* Do you mean eager1?

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-04-20 16:55:32

*Thread Reply:* And thanks :)

Nico Rascovan (nicorasco@gmail.com)
2021-03-16 16:45:07

Congratulations!

❤️ James Fellows Yates
Maxime Borry (maxime.borry@gmail.com)
2021-03-25 08:46:11

PyDamage: automated ancient damage identification and estimation for contigs in ancient DNA de novo assembly - https://www.biorxiv.org/content/10.1101/2021.03.24.436838v1

bioRxiv
PyDamage: automated ancient damage identification and estimation for contigs in ancient DNA de novo assembly
DNA de novo assembly can be used to reconstruct longer stretches of DNA (contigs), including genes and even genomes, from short DNA sequencing reads. Applying this technique to metagenomic data derived from archaeological remains, such as paleofeces and dental calculus, we can investigate past microbiome functional diversity that may be absent or underrepresented in the modern microbiome gene catalogue. However, compared to modern samples, ancient samples are often burdened with environmental contamination, resulting in metagenomic datasets that represent mixtures of ancient and modern DNA. The ability to rapidly and reliably establish the authenticity and integrity of ancient samples is essential for ancient DNA studies, and the ability to distinguish between ancient and modern sequences is particularly important for ancient microbiome studies. Characteristic patterns of ancient DNA damage, namely DNA fragmentation and cytosine deamination (observed as C-to-T transitions) are typically used to authenticate ancient samples and sequences. However, existing tools for inspecting and filtering aDNA damage either compute it at the read level, which leads to high data loss and lower quality when used in combination with de novo assembly, or require manual inspection, which is impractical for ancient assemblies that typically contain tens to hundreds of thousands of contigs. To address these challenges, we designed PyDamage, a robust, automated approach for aDNA damage estimation and authentication of de novo assembled aDNA. PyDamage uses a likelihood ratio based approach to discriminate between truly ancient contigs and contigs originating from modern contamination. We test PyDamage on both simulated, and empirical aDNA data from archaeological paleofeces, and we demonstrate its ability to reliably and automatically identify contigs bearing DNA damage characteristic of aDNA. Coupled with aDNA de novo assembly, PyDamage opens up new doors to explore functional diversity in ancient metagenomic datasets. ### Competing Interest Statement The authors have declared no competing interest.
Original URL: https://www.biorxiv.org/content/10.1101/2021.03.24.436838v1
🚀 James Fellows Yates
🤸‍♀️:skin_tone_3: Anna F.
👏 Katerina Guschanski, Pete Heintzman, aidanva, Nico Rascovan, Nikolay Oskolkov
🎉 ivelsko, Pete Heintzman, Nico Rascovan
aidanva (aida.andrades@gmail.com)
2021-03-25 10:32:43

Hi! I was wondering if someone has access to this paper: https://www.sciencedirect.com/science/article/abs/pii/S0966842X21000445 and wouldn't mind sharing the pdf??

sciencedirect.com
Development of Phylodynamic Methods for Bacterial Pathogens
Phylodynamic methods have been essential to understand the interplay between the evolution and epidemiology of infectious diseases. To date, the field…
Original URL: https://www.sciencedirect.com/science/article/abs/pii/S0966842X21000445
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-03-25 10:40:28

*Thread Reply:* https://paperpile.com/shared/hV5rn8

Paperpile
Development of Phylodynamic Methods for Bacterial Pathogens
Ingle DJ, et al. Trends Microbiol., 2021 ABSTRACT: Phylodynamic methods have been essential to understand the interplay between the evolution and epidemiology of infectious diseases. To date, the field has centered on viruses. Bacterial pathogens are seldom analyzed under such phylodynamic frameworks, due to their complex genome evolution and, until recently, a paucity of whole-genome sequence data sets with rich associated metadata. We posit that the increasing availability of bacterial genomes and epidemiological data means that the field is now ripe to lay the foundations for applying phylodynamics to bacterial pathogens. The development of new methods that integrate more complex genomic and ecological data will help to inform public heath surveillance and control strategies for bacterial pathogens that represent serious threats to human health.
Original URL: https://paperpile.com/shared/hV5rn8
aidanva (aida.andrades@gmail.com)
2021-03-25 14:29:48

*Thread Reply:* Thank you!

Nico Rascovan (nicorasco@gmail.com)
2021-03-31 16:57:44

May worth checking this method out: https://www.nature.com/articles/s41587-021-00861-3

Nature Biotechnology
A unified haplotype-based method for accurate and comprehensive variant calling
Octopus detects germline and somatic variants with high sensitivity and accuracy.
Original URL: https://www.nature.com/articles/s41587-021-00861-3
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-04-02 20:07:18

https://twitter.com/NikolayOskolkov/status/1378021308311683072?s=19

Really nice blog post from @Nikolay Oskolkov on being careful when reporting detection of pathogens in aDNA data!

twitter
} Nikolay Oskolkov (https://twitter.com/NikolayOskolkov/status/1378021308311683072)
I just published Plague in Ancient and Modern DNA at Medium / Towards Data Science <https://link.medium.com/aUwOG0Bf8eb>
Original URL: https://twitter.com/NikolayOskolkov/status/1378021308311683072?s=19
Twitter
🙌 Sterling Wright, Maxime Borry
Nikolay Oskolkov (nikolay.oskolkov@scilifelab.se)
2021-04-02 20:07:22

@Nikolay Oskolkov has joined the channel

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2021-04-02 20:09:35

this is a very good complement to @Nikolay Oskolkov post https://instrain.readthedocs.io/en/latest/important_concepts.html

👍 James Fellows Yates, Nikolay Oskolkov
Pete Heintzman (peteheintzman@gmail.com)
2021-04-15 22:11:50

https://science.sciencemag.org/content/early/2021/04/14/science.abf1667

Science
Unearthing Neanderthal population history using nuclear and mitochondrial DNA from cave sediments
Bones and teeth are important sources of Pleistocene hominin DNA, but are rarely recovered at archaeological sites. Mitochondrial DNA has been retrieved from cave sediments, but provides limited value for studying population relationships. We therefore developed methods for the enrichment and analysis of nuclear DNA from sediments, and applied them to cave deposits in western Europe and southern Siberia dated to between approximately 200,000 and 50,000 years ago. We detect a population replacement in northern Spain approximately 100,000 years ago, accompanied by a turnover of mitochondrial DNA. We also identify two radiation events in Neanderthal history during the early part of the Late Pleistocene. Our work lays the ground for studying the population history of ancient hominins from trace amounts of nuclear DNA in sediments.
Original URL: https://science.sciencemag.org/content/early/2021/04/14/science.abf1667
👍 Nikolay Oskolkov, Katerina Guschanski, James Fellows Yates
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-05-12 18:44:19

https://www.nature.com/articles/s41586-021-03532-0

Nature
Reconstruction of ancient microbial genomes from the human gut
Ancient microbiomes from palaeofaeces are more similar to non-industrialized than industrialized human gut microbiomes regardless of geography, but 39% of their de novo reconstructed genomes represent previously undescribed microbial species.
Original URL: https://www.nature.com/articles/s41586-021-03532-0
👍 Nikolay Oskolkov, Sterling Wright
🎉 Anna F., Pooja Swali
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-05-12 18:44:45

*Thread Reply:* @Katerina Guschanski this is the one I was talking about. I've not read it yet so can't say if it's the thing I was talking about

Katerina Guschanski (katerina.guschanski@ebc.uu.se)
2021-05-12 20:18:42

*Thread Reply:* Super! Thanks. Will have a look

Nico Rascovan (nicorasco@gmail.com)
2021-05-12 21:56:06

Have you seen this one? It’s from a guy I know…. Very cool work! https://www.pnas.org/content/118/20/e2021655118

👍 Nikolay Oskolkov, aidanva, Sterling Wright
👏:skin_tone_2: Kelly Blevins
:partyparrot: Anna F., Shreya
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-05-12 22:02:06

I dunno, I wouldn't trust him. He is pushing a veganist agenda that is a part of the 'great reset plan' apparently.

https://www.sott.net/article/452571-Oral-microbiomes-of-Neanderthals-primates-and-humans-reconstructed-revealing-insights-into-early-human-behaviour#comment365470

Sott.net
Oral microbiomes of Neanderthals, primates, and humans...
Living in and on our bodies are trillions of microbial cells belonging to thousands of bacterial species, known as the microbiome. These microbes play key roles in human health, but little is...
Original URL: https://www.sott.net/article/452571-Oral-microbiomes-of-Neanderthals-primates-and-humans-reconstructed-revealing-insights-into-early-human-behaviour#comment365470
🤣 aidanva, Shreya
🌱 Shreya
Nico Rascovan (nicorasco@gmail.com)
2021-05-12 22:12:48

hahaha

Nico Rascovan (nicorasco@gmail.com)
2021-05-12 23:41:56

Now I read all the comments below! They are even better than the article! hahaha So good… You must be proud James….

💪 James Fellows Yates
Abby Gancz (agancz@gmail.com)
2021-06-09 17:15:55

*Thread Reply:*

1-s2.0-S0966842X20303279-main.pdf
👍 Christina Warinner
❤️ Åshild (Ash)
Katerina Guschanski (katerina.guschanski@ebc.uu.se)
2021-06-09 17:16:22

*Thread Reply:* Haha, @Abby Gancz was 2 seconds faster than me 🙂!

😆 Åshild (Ash)
👍 Abby Gancz
Åshild (Ash) (ashild.v@gmail.com)
2021-06-09 17:17:55

*Thread Reply:* Thank you!!! So speedy :donut_parrot:

Katerina Guschanski (katerina.guschanski@ebc.uu.se)
2021-06-14 12:27:19

*Thread Reply:* Thank you!

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-06-14 14:49:57

For any American**/SRA users: this might be useful for generating standardised (following GCS) metadata tables for your studies: https://metagenote.niaid.nih.gov/

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-06-21 08:33:25

Attempt at Malaria capture: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8202054/

PubMed Central (PMC)
The elusive parasite: comparing macroscopic, immunological, and genomic approaches to identifying malaria in human skeletal remains from Sayala, Egypt (third to sixth centuries AD)
Although malaria is one of the oldest and most widely distributed diseases affecting humans, identifying and characterizing its presence in ancient human remains continue to challenge researchers. We attempted to establish a reliable approach to detecting ...
Original URL: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8202054/
👍 Nikolay Oskolkov
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-06-22 08:50:47

Ozga, A. T. and Ottoni, C. (2021) ‘Dental calculus as a proxy for animal microbiomes’, Quaternary international: the journal of the International Union for Quaternary Research. doi: 10.1016/j.quaint.2021.06.012. PDF: https://paperpile.com/shared/jt464e

Paperpile
Dental calculus as a proxy for animal microbiomes
Ozga AT, et al. Quat. Int., 2021 ABSTRACT: The field of dental calculus research has exploded in recent years, predominantly due to the multitude of studies related to human genomes and oral pathogens. Despite having a subset of these studies devoted to non-human primates, little progress has been made in the distribution of oral pathogens across domestic and wild animal populations. This overlooked avenue of research is particularly important at present when many animal populations with the potentiality for zoonotic transmission continue to reside in close proximity to human groups due to reasons such as deforestation and climatic impacts on resource availability. Here, we analyze previously all available published oral microbiome data recovered from the skeletal remains of animals, all of which belong to the Mammalia class. Our genus level results emphasize the tremendous diversity of oral ecologies across mammals in spite of the clustering based primarily on host species. We also discuss the caveats and flaws in analyzing ancient animal oral microbiomes at the species level of classification. Lastly, we assess the benefits, challenges, and gaps in the current knowledge of dental calculus research within animals and postulate the future of the field as a whole.
Original URL: https://paperpile.com/shared/jt464e
👍 Nikolay Oskolkov
Pete Heintzman (peteheintzman@gmail.com)
2021-06-23 17:33:21

https://www.nature.com/articles/s41586-021-03675-0

Nature
Pleistocene sediment DNA reveals hominin and faunal turnovers at Denisova Cave
Ancient mitochondrial DNA from sediments reveals the sequence of Denisovan, Neanderthal and faunal occupation of Denisova Cave, and evidence for the appearance of modern humans at least 45,000 years ago.
Original URL: https://www.nature.com/articles/s41586-021-03675-0
👍 Nikolay Oskolkov, James Fellows Yates, Becky Cribdon
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-06-30 19:02:03

https://www.cell.com/cell-reports/fulltext/S2211-1247(21)00645-8?returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS2211124721006458%3Fshowall%3Dtrue#%20|https://www.cell.com/cell-reports/fulltext/S2211-1247(21)00645-8?returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS2211124721006458%3Fshowall%3Dtrue#%20

Cell Reports
A 5,000-year-old hunter-gatherer already plagued by Yersinia pestis
Susat et al. reconstruct the genome of a 5,000-year-old Yersinia pestis strain detected in a hunter-gatherer from Latvia. The results show that the basal lineages evolved already at the beginning of the Neolithic and had presumably limited infection potential, suggesting isolated zoonotic events as causative triggers.
Original URL: https://www.cell.com/cell-reports/fulltext/S2211-1247(21)00645-8?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS2211124721006458%3Fshowall%3Dtrue#%20
🧐 Nico Rascovan
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-06-30 19:02:23

https://www.biorxiv.org/content/10.1101/2021.06.28.450199v1

bioRxiv
31,600-year-old human virus genomes support a Pleistocene origin for common childhood infections
The origins of viral pathogens and the age of their association with humans remains largely elusive. To date, there is no direct evidence about the diversity of viral infections in early modern humans pre-dating the Holocene. We recovered two near-complete genomes (5.2X and 0.7X) of human adenovirus C (HAdV-C), as well as low-coverage genomes from four distinct species of human herpesvirus obtained from two 31,630-year-old milk teeth excavated at Yana, in northeastern Siberia. Phylogenetic analysis of the two HAdV-C genomes suggests an evolutionary origin around 700,000 years ago consistent with a common evolutionary history with hominin hosts. Our findings push back the earliest direct molecular evidence for human viral infections by ∼25,000 years, and demonstrate that viral species causing common childhood viral infections today have been in circulation in humans at least since the Pleistocene. ### Competing Interest Statement The authors have declared no competing interest.
Original URL: https://www.biorxiv.org/content/10.1101/2021.06.28.450199v1
👍 Nico Rascovan
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-07-27 07:23:04

https://doi.org/10.1073/pnas.2102116118

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-07-27 07:23:40

Via retweet from @Zandra Fagernäs

👍 Nikolay Oskolkov
Nico Rascovan (nicorasco@gmail.com)
2021-07-27 11:18:06

very cool!

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-07-27 14:19:15

Congrats to @Maxime Borry @Alex Hübner @Christina Warinner

https://peerj.com/articles/11845/

PeerJ
PyDamage: automated ancient damage identification and estimation for contigs in ancient DNA de novo assembly
DNA de novo assembly can be used to reconstruct longer stretches of DNA (contigs), including genes and even genomes, from short DNA sequencing reads. Applying this technique to metagenomic data derived from archaeological remains, such as paleofeces and dental calculus, we can investigate past microbiome functional diversity that may be absent or underrepresented in the modern microbiome gene catalogue. However, compared to modern samples, ancient samples are often burdened with environmental contamination, resulting in metagenomic datasets that represent mixtures of ancient and modern DNA. The ability to rapidly and reliably establish the authenticity and integrity of ancient samples is essential for ancient DNA studies, and the ability to distinguish between ancient and modern sequences is particularly important for ancient microbiome studies. Characteristic patterns of ancient DNA damage, namely DNA fragmentation and cytosine deamination (observed as C-to-T transitions) are typically used to authenticate ancient samples and sequences, but existing tools for inspecting and filtering aDNA damage either compute it at the read level, which leads to high data loss and lower quality when used in combination with de novo assembly, or require manual inspection, which is impractical for ancient assemblies that typically contain tens to hundreds of thousands of contigs. To address these challenges, we designed PyDamage, a robust, automated approach for aDNA damage estimation and authentication of de novo assembled aDNA. PyDamage uses a likelihood ratio based approach to discriminate between truly ancient contigs and contigs originating from modern contamination. We test PyDamage on both on simulated aDNA data and archaeological paleofeces, and we demonstrate its ability to reliably and automatically identify contigs bearing DNA damage characteristic of aDNA. Coupled with aDNA de novo assembly, Pydamage opens up new doors to explore functional diversity in ancient metagenomic datasets.
Original URL: https://peerj.com/articles/11845/
:mask_parrot: Maxime Borry, Zandra Fagernäs, Sterling Wright, Raphael Eisenhofer
🤩 Christina Warinner, Arumi Mendoza
👏 Nico Rascovan, Nikolay Oskolkov, Pete Heintzman, Katerina Guschanski
👍 Lucy van Dorp, Åshild (Ash)
Katerina Guschanski (katerina.guschanski@ebc.uu.se)
2021-08-19 17:01:50

Big congrats on the pre-print @Zandra Fagernäs and co-authors! It is such a cool and important study! Will be our citation staple 🙂 https://www.biorxiv.org/content/10.1101/2021.08.16.456492v1

bioRxiv
Understanding the microbial biogeography of ancient human dentitions to guide study design and interpretation
The oral cavity is a heterogeneous environment, varying in factors such as pH, oxygen levels, and salivary flow. These factors affect the microbial community composition and distribution of species in dental plaque, but it is not known how well these patterns are reflected in archaeological dental calculus. In most archaeological studies, a single sample of dental calculus is studied per individual and is assumed to represent the entire oral cavity. However, it is not known if this sampling strategy introduces biases into studies of the ancient oral microbiome. Here, we present the results of a shotgun metagenomic study of a dense sampling of dental calculus from four Chalcolithic individuals from the southeast Iberian peninsula (ca. 4500-5000 BP). Inter-individual differences in microbial composition are found to be much larger than intra-individual differences, indicating that a single sample can indeed represent an individual in most cases. However, there are minor spatial patterns in species distribution within the oral cavity that should be taken into account when designing a study or interpreting results. Finally, we show that plant DNA identified in the samples may be of environmental origin, showing the importance of including environmental controls or several lines of biomolecular evidence. ### Competing Interest Statement The authors have declared no competing interest.
Original URL: https://www.biorxiv.org/content/10.1101/2021.08.16.456492v1
👍 Nikolay Oskolkov, Zandra Fagernäs, Sterling Wright
:mask_parrot: James Fellows Yates, Åshild (Ash)
👏:skin_tone_2: Kelly Blevins
😃 Miriam Bravo
👏 Christina Warinner
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-08-25 17:41:25

Congrats to @Jaelle Brealey (or is it @Jaelle Brealey?) And @Katerina Guschanski!

https://www.sciencedirect.com/science/article/pii/S096098222101112X

sciencedirect.com
The oral microbiota of wild bears in Sweden reflects the history of antibiotic use by humans
Following the advent of industrial-scale antibiotic production in the 1940s,1 antimicrobial resistance (AMR) has been on the rise and now poses a majo…
Original URL: https://www.sciencedirect.com/science/article/pii/S096098222101112X
👏 aidanva, Zandra Fagernäs, Pete Heintzman, Nikolay Oskolkov, Pooja Swali, Åshild (Ash), Ele
😊 Jaelle Brealey
🎉 Miriam Bravo
Jaelle Brealey (jcbrealey@gmail.com)
2021-08-25 17:41:33

@Jaelle Brealey has joined the channel

Jaelle Brealey (jaelle.brealey@ntnu.no)
2021-08-25 17:41:33

@Jaelle Brealey has joined the channel

Nico Rascovan (nicorasco@gmail.com)
2021-09-08 12:11:54

https://genome.cshlp.org/content/early/2021/09/03/gr.275777.121.abstract

genome.cshlp.org
Efficient computation of Faith's phylogenetic diversity with applications in characterizing microbiomes
An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms
Original URL: https://genome.cshlp.org/content/early/2021/09/03/gr.275777.121.abstract
👍 Maria Spyrou, Nikolay Oskolkov, James Fellows Yates, Lucy van Dorp
Nico Rascovan (nicorasco@gmail.com)
2021-09-08 12:12:26

A potentially cool alpha diversity metric to implement in microbiomes characterizations

Nico Rascovan (nicorasco@gmail.com)
2021-09-17 12:22:30

https://www.nature.com/articles/s41586-021-03798-4

Nature
Dairying enabled Early Bronze Age Yamnaya...
Nature - Analysis of ancient proteins suggests that Early Bronze Age dairying and horse domestication catalysed eastern Yamnaya migrations.
Original URL: https://www.nature.com/articles/s41586-021-03798-4
👍 Nikolay Oskolkov, Åshild (Ash)
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-09-22 11:18:40

https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1009886

journals.plos.org
A 3,000-year-old, basal S. enterica lineage from Bronze Age Xinjiang suggests spread along the Proto-Silk Road
Author summary Recent studies that use DNA extracted from ancient human remains have shown that the bacterial pathogen Salmonella enterica has infected humans since prehistoric times. Expanding the knowledge about its geographic spread and genetic diversity we reconstructed six ancient Salmonella genomes from individuals excavated at the Bronze Age Quanergou cemetery in Xinjiang, China. Our analysis shows that this form of Salmonella was closely related to a type that today specifically infects humans and/or pigs. However, based on our genetic assessment we determined that our ancient strains were not host adapted yet. Furthermore, we could show that in the course of its evolution the bacterium acquired some important virulence factors earlier than previously thought. Interpreting our results within an archaeological context we suggest that in Bronze Age Eastern Eurasia the spread of this pathogen was likely promoted through trade networks referred to as the Proto-Silk Road.
Original URL: https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1009886
👍 Nikolay Oskolkov, Lucy van Dorp, Åshild (Ash), Sterling Wright, Maria Lopopolo, Christina Warinner, Yoko Fukuhara, Barbara
😮 Miriam Bravo
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-09-22 11:19:03

Ancient Chinese S. enterica

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-10-04 13:11:54

Congrats to @Lena G @Kun Huang!

https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-021-01132-8

Microbiome
Metagenomic analysis of ancient dental calculus reveals unexplored diversity of oral archaeal Methanobrevibacter - Microbiome
Background Dental calculus (mineralised dental plaque) preserves many types of microfossils and biomolecules, including microbial and host DNA, and ancient calculus are thus an important source of information regarding our ancestral human oral microbiome. In this study, we taxonomically characterised the dental calculus microbiome from 20 ancient human skeletal remains originating from Trentino-South Tyrol, Italy, dating from the Neolithic (6000–3500 BCE) to the Early Middle Ages (400–1000 CE). Results We found a high abundance of the archaeal genus Methanobrevibacter in the calculus. However, only a fraction of the sequences showed high similarity to Methanobrevibacter oralis, the only described Methanobrevibacter species in the human oral microbiome so far. To further investigate the diversity of this genus, we used de novo metagenome assembly to reconstruct 11 Methanobrevibacter genomes from the ancient calculus samples. Besides the presence of M. oralis in one of the samples, our phylogenetic analysis revealed two hitherto uncharacterised and unnamed oral Methanobrevibacter species that are prevalent in ancient calculus samples sampled from a broad range of geographical locations and time periods. Conclusions We have shown the potential of using de novo metagenomic assembly on ancient samples to explore microbial diversity and evolution. Our study suggests that there has been a possible shift in the human oral microbiome member Methanobrevibacter over the last millennia. Video abstract
Original URL: https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-021-01132-8
🍻 Kun Huang
👍 Åshild (Ash), Jasmin Frangenberg, Nikolay Oskolkov
🎉 Miriam Bravo, Nico Rascovan, Yoko Fukuhara, Viridiana Villa
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-10-08 11:20:41

https://www.science.org/doi/10.1126/science.abi5658

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-10-08 11:22:35

137 Hep. B virus genomes, with the co-author list including @Maria Spyrou @Felix Key @Gunnar Neumann @Kerttu Majander @Susanna Sabin @Megan Michel @Betsy Nelson @Marcel Keller @Karen Giffin and probably a bunch of other people I missed because going through 171 authors is a tad too much

👍 Nikolay Oskolkov
Gunnar Neumann (gunnar_neumann@eva.mpg.de)
2021-10-08 11:24:13

https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-021-01120-2

BMC Biology
Mycobacterium leprae diversity and population dynamics in medieval Europe from novel ancient genomes - BMC Biology
Background Hansen’s disease (leprosy), widespread in medieval Europe, is today mainly prevalent in tropical and subtropical regions with around 200,000 new cases reported annually. Despite its long history and appearance in historical records, its origins and past dissemination patterns are still widely unknown. Applying ancient DNA approaches to its major causative agent, Mycobacterium leprae, can significantly improve our understanding of the disease’s complex history. Previous studies have identified a high genetic continuity of the pathogen over the last 1500 years and the existence of at least four M. leprae lineages in some parts of Europe since the Early Medieval period. Results Here, we reconstructed 19 ancient M. leprae genomes to further investigate M. leprae’s genetic variation in Europe, with a dedicated focus on bacterial genomes from previously unstudied regions (Belarus, Iberia, Russia, Scotland), from multiple sites in a single region (Cambridgeshire, England), and from two Iberian leprosaria. Overall, our data confirm the existence of similar phylogeographic patterns across Europe, including high diversity in leprosaria. Further, we identified a new genotype in Belarus. By doubling the number of complete ancient M. leprae genomes, our results improve our knowledge of the past phylogeography of M. leprae and reveal a particularly high M. leprae diversity in European medieval leprosaria. Conclusions Our findings allow us to detect similar patterns of strain diversity across Europe with branch 3 as the most common branch and the leprosaria as centers for high diversity. The higher resolution of our phylogeny tree also refined our understanding of the interspecies transfer between red squirrels and humans pointing to a late antique/early medieval transmission. Furthermore, with our new estimates on the past population diversity of M. leprae, we gained first insights into the disease’s global history in relation to major historic events such as the Roman expansion or the beginning of the regular transatlantic long distance trade. In summary, our findings highlight how studying ancient M. leprae genomes worldwide improves our understanding of leprosy’s global history and can contribute to current models of M. leprae’s worldwide dissemination, including interspecies transmissions.
Original URL: https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-021-01120-2
👀 Kelly Blevins
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-10-08 11:24:45

*Thread Reply:* ANOTHER! Could you add as an issue to AncientMetageomeDir bitte? 🙏

👍 Åshild (Ash)
Åshild (Ash) (ashild.v@gmail.com)
2021-10-08 18:34:29

*Thread Reply:* I did it

❤️ James Fellows Yates, Gunnar Neumann
Felix Key (key@mpiib-berlin.mpg.de)
2021-10-08 11:25:02

@Felix Key has joined the channel

Megan Michel (megan_michel@g.harvard.edu)
2021-10-08 11:25:02

@Megan Michel has joined the channel

Karen Giffin (giffin@shh.mpg.de)
2021-10-08 11:25:02

@Karen Giffin has joined the channel

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-10-13 22:37:08

https://www.sciencedirect.com/science/article/pii/S0960982221012719

sciencedirect.com
Hallstatt miners consumed blue cheese and beer during the Iron Age and retained a non-Westernized gut microbiome until the Baroque period
We subjected human paleofeces dating from the Bronze Age to the Baroque period (18th century AD) to in-depth microscopic, metagenomic, and proteomic a…
Original URL: https://www.sciencedirect.com/science/article/pii/S0960982221012719
🙌 Sterling Wright, Mohamed Sarhan
🍻 Kun Huang
🎉 Miriam Bravo
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-10-13 22:39:06

And another! from @Mohamed Sarhan and @Kun Huang!

Mohamed Sarhan (mohamed.sarhan@eurac.edu)
2021-10-13 22:39:09

@Mohamed Sarhan has joined the channel

ivelsko (velsko@shh.mpg.de)
2021-10-29 10:42:49

From @Bjorn Bartholdy! https://www.biorxiv.org/content/10.1101/2021.10.27.466104v1.abstract?%3Fcollection=

bioRxiv
Investigating Biases Associated with Dietary Starch Incorporation and Retention with an Oral Biofilm Model
Dental calculus has proven to contain a wealth of information on the dietary habits of past populations. These insights have, to a large extent, been obtained by the extraction and identification of starch granules contained within the mineralised dental plaque from a wide range of regions and time periods. The scope of previous studies have been limited to microfossil extraction and identification to reconstruct dietary preferences from the archaeological record, and few studies have attempted to address the biases of starch retention in dental calculus. Those that have considered this problem have been limited to in vivo studies on modern humans and non-human primates. Here, we present a multispecies oral biofilm model, which allows experimental research on starch incorporation and retention to be conducted on in vitro dental calculus in a controlled laboratory setting. The biofilms were exposed to treatment solutions with known quantities of dietary starches (wheat and potato) during the 25-day growth period. After this, the starch granules were extracted from the mature biofilm (by dissolution in EDTA), and counted. We show that the granule counts extracted from the model dental calculus represented a low proportion (ranging from 0.06% to 0.16%) of the total number of granules exposed to the biofilms throughout the experiment. Additionally, we found that the ratios of granule sizes from the extracted starch granules differed from the original treatment solutions, with large granules (&gt;20 μm) consistently being under-represented. We also found a correlation between the absolute granule counts and dry-weight of the biofilm ( r = 0.66, 90%CI[0.46,0.79]), as well as between the concentration (count per mg) of granules and dry-weight ( r = 0.30, 90%CI[0.06,0.51]). Our results reinforce previous in vivo studies suggesting that dental calculus presents a very small, and partly biased picture of the original dietary intake of starches, with an over-representation of plants producing granules smaller than 20 μm in size. The experimental model presented here is well-suited to address the need for further validation of methods and biases associated with dietary research on dental calculus. ### Competing Interest Statement The authors have declared no competing interest.
Original URL: https://www.biorxiv.org/content/10.1101/2021.10.27.466104v1.abstract?%3Fcollection=
👏 James Fellows Yates, Katerina Guschanski
:partyparrot: James Fellows Yates, Zandra Fagernäs
😁 Bjorn Bartholdy
Bjorn Bartholdy (bpbartholdy@pm.me)
2021-10-29 10:42:55

@Bjorn Bartholdy has joined the channel

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-11-10 16:21:58

https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3001421

journals.plos.org
Exploring bacterial diversity via a curated and searchable snapshot of archived DNA sequences
This study presents the first uniformly assembled, comprehensively described and searchable dataset of 661,405 bacterial genomes; this resource will empower more scientists to harness the multitude of data in public sequencing archives, but also reveals the biased composition of these archives, with 90% of the data originating from just 20 species.
Original URL: https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3001421
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-11-10 16:22:22

Careful of finding 'pathogens' in Metagenomic screening ;)

👍 Nikolay Oskolkov
Nikolay Oskolkov (nikolay.oskolkov@scilifelab.se)
2021-11-10 17:10:21

Ha-ha, this is brilliant @James Fellows Yates! Nowadays it is so easy to find pathogens by doing absolutely legal (or at least justifiable) manipulations with reference databases :))) so that report is not surprising ;)

😬 James Fellows Yates
Meriam Guellil (meriam.guellil.ac@gmail.com)
2021-11-10 17:17:23

Or basing the identification on a partial mapping and a metagenomic hit...

👍 Nikolay Oskolkov
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-11-10 17:17:40

*Thread Reply:* I sense a sub-tweet here 😉

😶 Meriam Guellil, Nikolay Oskolkov
🤣 Nikolay Oskolkov
Kelly Blevins (blevinske1@gmail.com)
2021-11-20 22:44:25

Exciting multidisciplinary work by @Meriam Guellil and co-authors

https://www.nature.com/articles/s41598-021-98214-2

Scientific Reports
Bioarchaeological insights into the last plague...
Scientific Reports - &lt;ArticleTitle Language=&amp;quot;En&amp;quot; OutputMedium=&amp;quot;All&amp;quot; xml:lang=&amp;quot;en&amp;quot;&gt;Bioarchaeological insights into the last plague...
Original URL: https://www.nature.com/articles/s41598-021-98214-2
👍 Nikolay Oskolkov, Sterling Wright, Bjorn Bartholdy
👍:skin_tone_3: Katerina Guschanski
🙂 Meriam Guellil
ivelsko (velsko@shh.mpg.de)
2021-11-22 11:20:58

We might have seen this in pre-print, but here's the final version https://www.nature.com/articles/s41591-021-01552-x

Nature Medicine
Reporting guidelines for human microbiome...
Nature Medicine - The STORMS tool provides guidance for concise and complete reporting of microbiome studies to facilitate manuscript preparation, peer review, reader comprehension of publications,...
Original URL: https://www.nature.com/articles/s41591-021-01552-x
👍 James Fellows Yates
ivelsko (velsko@shh.mpg.de)
2021-11-22 11:22:02

*Thread Reply:* Oooohhhh "presented as an editable table for inclusion in supplementary materials"

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-11-22 11:22:06

*Thread Reply:* Definitely need to read this

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-11-22 11:22:08

*Thread Reply:* OOHHH

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-11-22 11:22:22

*Thread Reply:* Now to find time to actually read it

ivelsko (velsko@shh.mpg.de)
2021-11-22 11:23:03

*Thread Reply:* At this stage in your career, you should be training to just absorb papers, no more time wasted "reading"

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-11-22 16:47:44

*Thread Reply:* Ok, find time to absorb 😆

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-11-25 09:11:23

*Thread Reply:* Ok did it

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-11-25 09:11:58

*Thread Reply:* I don't think it matches what I immediately want for the standardised metadata sheet, but certainly it's something that we should aim for in the future 👍

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-11-25 09:13:08

*Thread Reply:* basically it tells you 'how to write your paper' for a specific type of microibome study, which might not necessarily work for our field at the moment (exactly). But certainly we could adopt some of these things.

It's just a shame they've saved it as shitty DOCX/XLSX files and not something under version control, so it would make it harder to fork and modify

ivelsko (velsko@shh.mpg.de)
2021-11-25 09:13:29

*Thread Reply:* Yeah it really is a check list and not a template for what to upload

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-11-25 09:13:34

*Thread Reply:* Yup

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-11-25 09:13:46

*Thread Reply:* The MIxS stuff is what we should aim for initially

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-11-25 09:13:51

*Thread Reply:* (and tools to make that easier)

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-12-15 20:55:30

https://www.mdpi.com/2079-7737/10/12/1324

MDPI
Genomic Analysis of 18th-Century Kazakh Individuals and Their Oral Microbiome
The Asian Central Steppe, consisting of current-day Kazakhstan and Russia, has acted as a highway for major migrations throughout history. Therefore, describing the genetic composition of past populations in Central Asia holds value to understanding human mobility in this pivotal region. In this study, we analyse paleogenomic data generated from five humans from Kuygenzhar, Kazakhstan. These individuals date to the early to mid-18th century, shortly after the Kazakh Khanate was founded, a union of nomadic tribes of Mongol Golden Horde and Turkic origins. Genomic analysis identifies that these individuals are admixed with varying proportions of East Asian ancestry, indicating a recent admixture event from East Asia. The high amounts of DNA from the anaerobic Gram-negative bacteria Tannerella forsythia, a periodontal pathogen, recovered from their teeth suggest they may have suffered from periodontitis disease. Genomic analysis of this bacterium identified recently evolved virulence and glycosylation genes including the presence of antibiotic resistance genes predating the antibiotic era. This study provides an integrated analysis of individuals with a diet mostly based on meat (mainly horse and lamb), milk, and dairy products and their oral microbiome.
Original URL: https://www.mdpi.com/2079-7737/10/12/1324
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-12-15 20:55:42

From @Toni de Dios Martínez et al!

😀 Toni de Dios Martínez
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-12-15 21:06:48

And also this preprint from @Katherine Eaton

https://www.researchsquare.com/article/rs-1146895/v1

Research Square
Plagued by a cryptic clock: Insight and issues from the global phylogeny of Yersinia pestis
Research Square is a preprint platform that makes research communication faster, fairer, and more useful.
Original URL: https://www.researchsquare.com/article/rs-1146895/v1
👍 Åshild (Ash), Nikolay Oskolkov
Katerina Guschanski (katerina.guschanski@ebc.uu.se)
2021-12-16 16:22:29

https://www.sciencedirect.com/science/article/pii/S1040618221005735

sciencedirect.com
Combined metagenomic and archaeobotanical analyses on human dental calculus: A cross-section of lifestyle conditions in a Copper Age population of central Italy
Multidisciplinary analyses on ancient dental calculus revealed the possibility to reconstruct habits and diet of ancient human populations, investigat…
Original URL: https://www.sciencedirect.com/science/article/pii/S1040618221005735
👍 Nikolay Oskolkov, Zoé Pochon, Bjorn Bartholdy
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-12-18 10:01:15

https://www.nature.com/articles/s41467-021-27542-8

Nature
Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows
Nature Communications - The authors present CAMPI, a large-scale multi-lab comparison of diverse metaproteomics workflows. CAMPI provides insights into the robustness of current methods, suggests...
Original URL: https://www.nature.com/articles/s41467-021-27542-8
👍 Anan Ibrahim
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-12-18 10:01:49

Maybe a good study to replciate for ancient meagneomics / ancient proteomics ☝️

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-12-21 16:25:53

https://journals.asm.org/eprint/X56YB6KCQVCCDS4Q9F3N/full

The legendary, mythical, fabled <#CPHECT30A|spaam2-open> opinion paper is now published in mSystems!

Thank you to everyone who attended :spaam: SPAAM2, and those who also gave further contributions, comments, and feedback for this paper. It was certainly more difficult than I expected since we proposed the idea - reflected in our challenges to pin down a single topic to talk about - however overall I think this reflects the exciting potential and movement happening in our field!

Let's hope the paper gets some interest from modern metagenomicists and open up some discussions!

I would like to also finish with a personal BIG shout-out and eternal gratitude to @Clio Der Sarkissian @Anna F. @Alex Hübner @Åshild (Ash) and @ivelsko, who put up with the never-ending series or meetings and re-writing over each others comments and suggestions on Google Docs! ❤️ you all!

🎉 Zandra Fagernäs, Katerina Guschanski, aidanva, Nikolay Oskolkov, Maria Spyrou, Meriam Guellil, Nihan D Dagtas, ivelsko, Maria Lopopolo, Pete Heintzman, Claudio Ottoni, Kelly Blevins, Christina Warinner
:partyparrot: Jasmin Frangenberg, Raphael Eisenhofer
🙌:skin_tone_6: Miriam Bravo
:spam_dance: Åshild (Ash)
Katerina Guschanski (katerina.guschanski@ebc.uu.se)
2021-12-21 16:38:36

*Thread Reply:* Brilliant! Huge congratulations to the team!

❤️ James Fellows Yates
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-12-21 16:45:55

Tweet coming later today!

Nico Rascovan (nicorasco@gmail.com)
2021-12-21 17:25:11

Congratulations!!

Nikolay Oskolkov (nikolay.oskolkov@scilifelab.se)
2021-12-21 17:57:37

Congratulations!

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-12-21 19:12:31

Oops, sorry - apparently that link was a 'author sharing one' that only has 10 download limits 😆 . Could someone send me the PDF if they downloaded it?

😂 aidanva
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-12-21 19:14:21

Wait got it - nevermind!

Åshild (Ash) (ashild.v@gmail.com)
2021-12-21 20:51:55

Proper link here 😉: https://journals.asm.org/doi/epub/10.1128/msystems.01315-21

❤️ James Fellows Yates, Maria Lopopolo, Nikolay Oskolkov
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-12-21 20:52:41

*Thread Reply:* Fecking hell I'm disorganised at the moment 🙄🤦‍♀️:skintone3:

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-12-21 20:52:45

*Thread Reply:* Thanks you!

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-01-24 17:47:42

Interesting looking preprint from @Meriam Guellil @Lucy van Dorp et al!

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-01-24 17:47:45

https://www.biorxiv.org/content/10.1101/2022.01.19.476912v1

bioRxiv
Ancient herpes simplex 1 genomes reveal recent viral structure in Eurasia
Human herpes simplex virus 1 (HSV-1), a life-long infection spread by oral contact, today infects a majority of adults globally, yet no ancient HSV-1 genomes have yet been published. Phylogeographic clustering of sampled diversity into European, pan-Eurasian, and African groups(Pfaff et al. 2016; Szpara, Tafuri, et al. 2014) has suggested that the virus co-diverged with anatomically modern humans migrating out of Africa(Kolb, Ane, and Brandt 2013), although a much younger origin has also been proposed(Forni et al. 2020). The lack of ancient HSV-1 genomes, high rates of recombination, and high mobility of humans in the modern era have impeded the understanding of HSV-1's evolutionary history. Here we present three full ancient European HSV-1 genomes and one partial genome, dating to between the 3rd and 17th century CE, sequenced to up to 9.5X with paired human genomes up to 10.16X. These HSV-1 strains fall within modern Eurasian diversity. We estimate a mean mutation rate of 7.6 x 10-7 - 1.13 x 10-6 for non-African diversity leading to an estimated age of sampled modern Eurasian diversity to 4.68 (3.87 - 5.65) kya. Extrapolation of these rates indicate the age of sampled HSV-1 to 5.29 (4.60-6.12 kya, suggesting lineage replacement coinciding with the late Neolithic and implicating Bronze Age migrations(Allentoft et al. 2015) in the distribution of HSV-1 through Eurasia. ### Competing Interest Statement The authors have declared no competing interest.
Original URL: https://www.biorxiv.org/content/10.1101/2022.01.19.476912v1
👀 Kelly Blevins, Nasreen Broomand, Zoé Pochon
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-01-25 17:35:51

From the newly joined @Eric Capo @Marie-Eve Monchamp @Linda Armbrecht!

one for #TeamDir 😉

https://sfamjournals.onlinelibrary.wiley.com/doi/10.1111/1462-2920.15913

☺️ Eric Capo
Eric Capo (eric.capo@hotmail.fr)
2022-01-25 17:57:45

*Thread Reply:* Thank you for sharing!

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-01-27 06:20:40

Next up on the 2022 preprints! @Pooja Swali et al. With ancient British plague!

https://www.biorxiv.org/content/10.1101/2022.01.26.477195v1

bioRxiv
Yersinia pestis genomes reveal plague in Britain 4,000 years ago
Extinct lineages of Yersinia pestis, the causative agent of the plague, have been identified in several individuals from Central Europe and Asia between 5,000 and 3,500 years before present (BP). One of these, the 'LNBA lineage' (Late Neolithic and Bronze Age), has been suggested to have spread into Central Europe with human groups expanding from the Eurasian steppes. Here, we show that LNBA plague was spread to Europe's northwestern periphery by sequencing Yersinia pestis genomes from two individuals dating to ~4,000 cal BP from an unusual mass burial context in Somerset, England, UK. This represents the earliest evidence of plague in Britain documented to date. These British Yersinia pestis genomes belong to a sublineage previously observed in two Bronze Age individuals from Central Europe that had lost the putative virulence factor yapC. This sublineage is later found in Central Asia ~3,600 BP. While the severity of disease is currently unclear, the wide geographic distribution within a few centuries suggests substantial transmissibility. ### Competing Interest Statement The authors have declared no competing interest.
Original URL: https://www.biorxiv.org/content/10.1101/2022.01.26.477195v1
🤩 aidanva, Nasreen Broomand
👍 Åshild (Ash), Meriam Guellil
👏 Christina Warinner
ivelsko (velsko@shh.mpg.de)
2022-01-31 12:38:38

Cautionary tale in ancient metagenomic dietary analysis https://www.biorxiv.org/content/10.1101/2022.01.26.472964v1.abstract?%3Fcollection=

bioRxiv
Neanderthals did not likely consume Physcomitrium patens – a model moss species
This manuscript is discussing the method of Weyrich et al., 2017, "Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus". When studying the dietary profile of a Neanderthal specimen from El Sidron cave (Spain) by sequencing ancient DNA present in calcified dental plaque (calculus) the authors identified a wide-range of potential food sources, including woolly rhinoceros, mushrooms, pine nuts, and moss - namely the less-than-abundant model species Physcomitrium patens. We doubted that Neanderthals were actually eating P. patens. By analyzing the ancient DNA reads using different mapping methods, we show likely a misinterpretation based on the previously used methods. The probability of Neanderthals eating P. patens is the same as eating rice or tomato. However, neither crop was grown in Europe at the time Neanderthals thrived. ### Competing Interest Statement The authors have declared no competing interest.
Original URL: https://www.biorxiv.org/content/10.1101/2022.01.26.472964v1.abstract?%3Fcollection=
👍 James Fellows Yates, Nikolay Oskolkov, Zandra Fagernäs, Sterling Wright, Pete Heintzman
👏:skin_tone_3: Katerina Guschanski
👏 Nasreen Broomand
Åshild (Ash) (ashild.v@gmail.com)
2022-02-01 11:32:45

https://www.biorxiv.org/content/10.1101/2022.01.27.477466v1?ct=

bioRxiv
Indigenous peoples in eastern Brazil: insights from 19th century genomes and metagenomes
Although Brazil was inhabited by more than 3,000 Indigenous populations prior to European colonization, today's Indigenous peoples represent less than 1% of Brazil's census population. Some of the decimated communities belonged to the so-called "Botocudos" from central-eastern Brazil. These peoples are thought to represent a case of long-standing genetic continuity bearing a strong craniometric resemblance to that of the oldest Indigenous Americans ("Paleoamericans"). Yet, little is known about their origins and genetic relationship to other Native Americans, as only two "Botocudo" genomes have been sequenced so far and those were surprisingly of Polynesian ancestry. To deepen our knowledge on the genomic history of pre-contact Indigenous Americans and the pathogens they were exposed to, we carbon-dated and sequenced 24 ancient Brazilians (including 22 "Botocudos") whose remains were hosted at the National Museum of Rio de Janeiro and recovered prior to the tragic 2018 fire. The resulting genomes' depth of coverage ranged from 0.001x to 24x. Their genetic ancestry was found to be Indigenous American without gene flow from external populations such as Europeans, Africans or Polynesians. Unlike Mesoamericans, the "Botocudos" and Amazonians do not seem to have experienced a population expansion once in the Americas. Moreover, remarkably, their genomes exhibit amongst the lowest levels of heterozygosity worldwide and long runs of homozygosity, which could be explained by unique social practices or a very small effective size. Finally, whole genomes of likely ancient pathogens were recovered, including lineages of human parvovirus B19 that were possibly introduced after the European contact. ### Competing Interest Statement The authors have declared no competing interest.
Original URL: https://www.biorxiv.org/content/10.1101/2022.01.27.477466v1?ct=
👍 James Fellows Yates, Nikolay Oskolkov, Maria Spyrou
👍:skin_tone_6: Miriam Bravo
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-02-03 05:46:21

https://mbmg.pensoft.net/article/78128/element/8/149541//

Metabarcoding and Metagenomics
Shifts in DNA yield and biological community composition in stored sediment: implications for paleogenomic studies
Lake sediments hold a wealth of information from past environments that is highly valuable for paleolimnological reconstructions. These studies increasingly apply modern molecular tools targeting sedimentary DNA (sedDNA). However, sediment core sampling can be logistically difficult, making immediate subsampling for sedDNA challenging. Sediment cores are often refrigerated (4 °C) for weeks or months before subsampling. We investigated the impact of storage time on changes in DNA (purified or as cell lysate) concentrations and shifts in biological communities following storage of lake surface sediment at 4 °C for up to 24 weeks. Sediment samples (~ 0.22 g, in triplicate per time point) were spiked with purified DNA (100 or 200 ng) or lysate from a brackish water cyanobacterium that produces the cyanotoxin nodularin or non-spiked. Samples were analysed every 1–4 weeks over a 24-week period. Droplet digital PCR showed no significant decrease in the target gene (nodularin synthetase – subunit F; ndaF) over the 24-week period for samples spiked with purified DNA, while copy number decreased by more than half in cell lysate-spiked samples. There was significant change over time in bacteria and eukaryotic community composition assessed using metabarcoding. Amongst bacteria, the cyanobacterial signal became negligible after 5 weeks while Proteobacteria increased. In the eukaryotic community, Cercozoa became dominant after 6 weeks. These data demonstrate that DNA yields and community composition data shift significantly when sediments are stored chilled for more than 5 weeks. This highlights the need for rapid subsampling and appropriate storage of sediment core samples for paleogenomic studies.
Original URL: https://mbmg.pensoft.net/article/78128/element/8/149541//
👍:skin_tone_6: Miriam Bravo
👍 Eric Capo, Pete Heintzman, Nikolay Oskolkov
aidanva (aida.andrades@gmail.com)
2022-02-03 10:39:34

Congrats @Meriam Guellil @Marcel Keller and @Freddi Scheib !! Very cool stuff!! https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02580-z

BioMed Central
An invasive Haemophilus influenzae serotype b infection in an Anglo-Saxon plague victim - Genome Biology
Background The human pathogen Haemophilus influenzae was the main cause of bacterial meningitis in children and a major cause of worldwide infant mortality before the introduction of a vaccine in the 1980s. Although the occurrence of serotype b (Hib), the most virulent type of H. influenzae, has since decreased, reports of infections with other serotypes and non-typeable strains are on the rise. While non-typeable strains have been studied in-depth, very little is known of the pathogen’s evolutionary history, and no genomes dating prior to 1940 were available. Results We describe a Hib genome isolated from a 6-year-old Anglo-Saxon plague victim, from approximately 540 to 550 CE, Edix Hill, England, showing signs of invasive infection on its skeleton. We find that the genome clusters in phylogenetic division II with Hib strain NCTC8468, which also caused invasive disease. While the virulence profile of our genome was distinct, its genomic similarity to NCTC8468 points to mostly clonal evolution of the clade since the 6th century. We also reconstruct a partial Yersinia pestis genome, which is likely identical to a published first plague pandemic genome of Edix Hill. Conclusions Our study presents the earliest genomic evidence for H. influenzae, points to the potential presence of larger genomic diversity in the phylogenetic division II serotype b clade in the past, and allows the first insights into the evolutionary history of this major human pathogen. The identification of both plague and Hib opens questions on the effect of plague in immunocompromised individuals already affected by infectious diseases.
Original URL: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02580-z
👍 Nikolay Oskolkov, Pooja Swali, Sterling Wright
👏 Nico Rascovan, Maria Spyrou, James Fellows Yates, Maria Lopopolo, Åshild (Ash)
👀 Kelly Blevins
👍:skin_tone_6: Miriam Bravo
Meriam Guellil (meriam.guellil.ac@gmail.com)
2022-02-03 10:44:33

*Thread Reply:* Thanks!

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-02-07 14:36:07

https://www.ncbi.nlm.nih.gov/labs/pmc/articles/PMC8805238/

PubMed Central (PMC)
In-situ sequencing reveals the effect of storage on lacustrine sediment microbiome demographics and functionality
The sediment microbiome is a demographically diverse and functionally active biosphere. Ensuring that data acquired from sediment is truly representative of the microbiome is critical to achieving robust analyses. Sample storage and the processing and ...
Original URL: https://www.ncbi.nlm.nih.gov/labs/pmc/articles/PMC8805238/
👍:skin_tone_6: Miriam Bravo
Nico Rascovan (nicorasco@gmail.com)
2022-02-14 12:44:04

https://www.nature.com/articles/s41559-021-01652-4

Of interest for the ancient plague community (not ancient DNA though)

Nature
Palaeoecological data indicates land-use changes across Europe linked to spatial heterogeneity in mortality during the Black Death pandemic
Nature Ecology &amp; Evolution - Historical accounts of the mortality outcomes of the Black Death plague pandemic are variable across Europe, with much higher death tolls suggested in some areas...
Original URL: https://www.nature.com/articles/s41559-021-01652-4
👍 Nikolay Oskolkov, James Fellows Yates
Miriam Bravo (bravolomiriam@gmail.com)
2022-02-15 00:08:19

Placing ancient DNA sequences into reference phylogenies https://watermark.silverchair.com/msac017.pdf?token=AQECAHi208BE49Ooan9kkhWErcy7Dm3ZL9C[…]yTxKbecBoJeLyWslx_TTOSg2BYFCGTtP-9wzaa8cdpy7DQq-k2YMcHiM

👍 Nikolay Oskolkov, James Fellows Yates, Pete Heintzman
Marcel Keller (marcel.keller@ut.ee)
2022-02-15 10:13:02

*Thread Reply:* link doesn’t work for me 😕

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-02-15 08:00:17

https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009838

journals.plos.org
Evaluating supervised and unsupervised background noise correction in human gut microbiome data
Author summary The human gut microbiome is known to play a major role in health and is associated with many diseases including colorectal cancer, obesity, and diabetes. The prediction of host phenotypes and identification of biomarkers of disease is essential for harnessing the therapeutic potential of the microbiome. However, many metagenomic datasets are affected by technical variables that introduce unwanted variation that can confound the ability to predict phenotypes and identify biomarkers. Currently, supervised methods originally designed for gene expression and RNA-seq data are commonly applied to microbiome data for correction of background noise, but they are limited in that they cannot correct for unmeasured sources of variation. Unsupervised approaches address this issue, but current methods are limited because they are ill-equipped to deal with the unique aspects of microbiome data, which is compositional, highly skewed, and sparse. We perform a comparative analysis of the ability of different denoising transformations in combination with supervised correction methods as well as an unsupervised principal component correction approach and find that all correction approaches reduce false positives for biomarker discovery. In the task of predicting phenotypes, different approaches have varying success where the unsupervised correction can improve prediction when technical variables contribute to the majority of variance in the data. As new and larger metagenomic datasets become increasingly available, background noise correction will become essential for generating reproducible microbiome analyses.
Original URL: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009838
Åshild (Ash) (ashild.v@gmail.com)
2022-03-01 14:40:17

https://www.sciencedirect.com/science/article/pii/S147297922200018X?via%3Dihub

sciencedirect.com
Metagenomic analysis reveals mixed Mycobacterium tuberculosis infection in a 18th century Hungarian midwife
The Vác Mummy Collection comprises 265 well documented mummified individuals from the late 16th to the early 18th century that were discovered in 1994…
Original URL: https://www.sciencedirect.com/science/article/pii/S147297922200018X?via%3Dihub
👀 Kelly Blevins
👍:skin_tone_6: Miriam Bravo
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-03-07 11:34:41

Congrats to @Åshild (Ash) on her new paper! (and thank you for the AncientMetagenomeDir Issue too :D)

Ancient TB from pre-contact S. American populations!

https://www.nature.com/articles/s41467-022-28562-8

Nature
Geographically dispersed zoonotic tuberculosis in pre-contact South American human populations
Nature Communications - ‘Pre-contact era humans from coastal South America were infected by Mycobacterium pinnipedii, most likely, through contact with infected pinnipeds. Here, the authors...
Original URL: https://www.nature.com/articles/s41467-022-28562-8
🎉 aidanva, Marcel Keller, Pete Heintzman, Pooja Swali, Gunnar Neumann, Bjorn Bartholdy, Christina Warinner, Zandra Fagernäs, Maria Spyrou, Sterling Wright, Meriam van Os, Anna F., Zoé Pochon, Nikolay Oskolkov
👍:skin_tone_2: Meriam Guellil
👍:skin_tone_3: Katerina Guschanski
🦭 Kelly Blevins, Anna F.
👏:skin_tone_2: Kelly Blevins
👏 Claudio Ottoni
🙌:skin_tone_6: Miriam Bravo
:partyparrot: Anna F.
Åshild (Ash) (ashild.v@gmail.com)
2022-03-07 16:33:49

*Thread Reply:* Thank you!!

Zandra Fagernäs (fagernaes@shh.mpg.de)
2022-03-19 18:31:51

Our paper "Understanding the microbial biogeography of ancient human dentitions to guide study design and interpretation" is finally out! 😄 https://academic.oup.com/femsmicrobes/article/doi/10.1093/femsmc/xtac006/6541847?login=false

❤️ aidanva, Bjorn Bartholdy, Gunnar Neumann, Alina Hiss, James Fellows Yates
🎉 Miriam Bravo, James Fellows Yates, Jasmin Frangenberg, Nikolay Oskolkov
:vikingparrot: Åshild (Ash), Katerina Guschanski
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-03-22 09:24:23

Might be of interest: https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.13608

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-03-22 09:24:41

"A Theoretical Analysis of Taxonomic Binning Accuracy "

👍 Nikolay Oskolkov
Katerina Guschanski (katerina.guschanski@ebc.uu.se)
2022-03-23 18:20:50

Beyond dirty teeth: Integrating dental calculus studies with osteoarchaeological parameters https://www.sciencedirect.com/science/article/pii/S1040618222000726

sciencedirect.com
Beyond dirty teeth: Integrating dental calculus studies with osteoarchaeological parameters
The study of ancient human dental calculus (mineralized dental plaque, also known as tartar) is becoming increasingly important in osteoarchaeology, h…
Original URL: https://www.sciencedirect.com/science/article/pii/S1040618222000726
👍 James Fellows Yates, Sterling Wright, Nikolay Oskolkov, Andrea quagliariello
👍:skin_tone_6: Miriam Bravo
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-03-25 20:24:55

https://peerj.com/articles/12784/

PeerJ
Benchmarking metagenomics classifiers on ancient viral DNA: a simulation study
Owing to technological advances in ancient DNA, it is now possible to sequence viruses from the past to track down their origin and evolution. However, ancient DNA data is considerably more degraded and contaminated than modern data making the identification of ancient viral genomes particularly challenging. Several methods to characterise the modern microbiome (and, within this, the virome) have been developed; in particular, tools that assign sequenced reads to specific taxa in order to characterise the organisms present in a sample of interest. While these existing tools are routinely used in modern data, their performance when applied to ancient microbiome data to screen for ancient viruses remains unknown. In this work, we conducted an extensive simulation study using public viral sequences to establish which tool is the most suitable to screen ancient samples for human DNA viruses. We compared the performance of four widely used classifiers, namely Centrifuge, Kraken2, DIAMOND and MetaPhlAn2, in correctly assigning sequencing reads to the corresponding viruses. To do so, we simulated reads by adding noise typical of ancient DNA to a set of publicly available human DNA viral sequences and to the human genome. We fragmented the DNA into different lengths, added sequencing error and C to T and G to A deamination substitutions at the read termini. Then we measured the resulting sensitivity and precision for all classifiers. Across most simulations, more than 228 out of the 233 simulated viruses were recovered by Centrifuge, Kraken2 and DIAMOND, in contrast to MetaPhlAn2 which recovered only around one third. Overall, Centrifuge and Kraken2 had the best performance with the highest values of sensitivity and precision. We found that deamination damage had little impact on the performance of the classifiers, less than the sequencing error and the length of the reads. Since Centrifuge can handle short reads (in contrast to DIAMOND and Kraken2 with default settings) and since it achieve the highest sensitivity and precision at the species level across all the simulations performed, it is our recommended tool. Regardless of the tool used, our simulations indicate that, for ancient human studies, users should use strict filters to remove all reads of potential human origin. Finally, we recommend that users verify which species are present in the database used, as it might happen that default databases lack sequences for viruses of interest.
Original URL: https://peerj.com/articles/12784/
👍:skin_tone_3: Katerina Guschanski, Meriam van Os
👍 Nikolay Oskolkov
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-04-13 12:58:53

As the authors are being shy:

https://www.pnas.org/doi/10.1073/pnas.2116722119

Congrats to @aidanva @Gunnar Neumann @Maria Spyrou !

🎉 Meriam Guellil, Marcel Keller, Pete Heintzman, Zandra Fagernäs, irinavelsko, Alina Hiss, Claudio Ottoni, Shreya, Nico Rascovan, Pooja Swali, I-Ting Huang, Christina Warinner, Katerina Guschanski, Sterling Wright, Nasreen Broomand, Zoé Pochon, Anna F., Bjorn Bartholdy, Maria Lopopolo
:vikingparrot: Åshild (Ash), Nico Rascovan, Jasmin Frangenberg, Katerina Guschanski
🦠 Åshild (Ash)
:mask_parrot: Megan Michel, Pooja Swali
🙌:skin_tone_6: Miriam Bravo
👏:skin_tone_2: Kelly Blevins
🙌:skin_tone_3: Meriam van Os
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-04-13 13:12:47

Plague, plague everywhere!

Maria Spyrou (spyrou@shh.mpg.de)
2022-04-13 14:46:58

Thanks guys! Very glad it’s out! Big congratulations to Aida, Gunnar and Lyazzat for all their work!

❤️ aidanva, Gunnar Neumann
aidanva (aida.andrades@gmail.com)
2022-04-13 14:47:42

Thank you!

Christina Warinner (warinner@shh.mpg.de)
2022-04-13 17:11:29

Great job @aidanva!

Nico Rascovan (nicorasco@gmail.com)
2022-04-13 17:19:09

I invited her to make the toast!

IMG_20220413_171817608.jpg
irinavelsko (irinavelsko@gmail.com)
2022-04-26 08:39:03

Curious about the kinds of biomedical questions that can be addressed with ancient dental calculus? How much does it reflect oral health? Just how much does community structure change concomitant with human cultural transitions? Check out our new preprint! https://www.biorxiv.org/content/10.1101/2022.04.25.489366v1

bioRxiv
Ancient dental calculus preserves signatures of biofilm succession and inter-individual variation independent of dental pathology
Dental calculus preserves oral microbes, enabling comparative studies of the oral microbiome and health through time. However, small sample sizes and limited dental health metadata have hindered health-focused investigations to date. Here we investigate the relationship between tobacco pipe smoking and dental calculus microbiomes. Dental calculus from 75 individuals from the 19th century Middenbeemster skeletal collection (Netherlands) were analyzed by metagenomics. Demographic and dental health parameters were systematically recorded, including the presence/number of pipe notches. Comparative data sets from European populations before and after the introduction of tobacco were also analyzed. Calculus species profiles were compared with oral pathology to examine associations between microbiome community, smoking behavior, and oral health status. The Middenbeemster individuals exhibited relatively poor oral health, with a high prevalence of periodontal disease, caries, heavy calculus deposits, and antemortem tooth loss. No associations between pipe notches and dental pathologies, or microbial species composition, were found. Calculus samples before and after the introduction of tobacco showed highly similar species profiles. Observed inter-individual microbiome differences were consistent with previously described variation in human populations from the Upper Paleolithic to the present. Dental calculus may not preserve microbial indicators of health and disease status as distinctly as dental plaque. ### Competing Interest Statement The authors have declared no competing interest.
Original URL: https://www.biorxiv.org/content/10.1101/2022.04.25.489366v1
🎉 Bjorn Bartholdy, I-Ting Huang, Zandra Fagernäs, Raphael Eisenhofer, Jasmin Frangenberg, Åshild (Ash), Nasreen Broomand, Sterling Wright
👏:skin_tone_3: Katerina Guschanski
👏 Claudio Ottoni, James Fellows Yates, Nikolay Oskolkov
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-05-03 08:29:54

We've started to have an uptick in follows on the SPAAM #twitter account - so I would like to make it a bit more active. I thought one way would be to post papers more regularly (e.g. Ancient Metagenomic Paper of the WEek) - would do people think about this paper: https://www.annualreviews.org/doi/abs/10.1146/annurev-phyto-021021-041830

Would that be a good one to share on Twitter?

👍 Christina Warinner, Andrea quagliariello, Nikolay Oskolkov, Sterling Wright, Laura Carrillo Olivas
👍:skin_tone_3: Katerina Guschanski
👍:skin_tone_6: Miriam Bravo
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-05-03 13:03:25

Ok scheduled! @channel please post new papers you come across here, and we can pick one each week to post on the twitter account 🙂. Bonus points if it's from SPAAM members!

👍 Jasmin Frangenberg, Nikolay Oskolkov, Sterling Wright, Zoé Pochon
👍:skin_tone_6: Miriam Bravo
Maxime Borry (maxime.borry@gmail.com)
2022-05-10 17:15:33

Not a paper, but following our discussion with @Nikolay Oskolkov @Zoé Pochon @Meriam Guellil, some playing with KrakenUniq https://maximeborry.com/post/kraken-uniq/

Maxime Borry
A new E-score for KrakenUniq | Maxime Borry
How to distinguish between true and false positive assignations with KrakenUniq
Original URL: https://maximeborry.com/post/kraken-uniq/
👍 Nikolay Oskolkov, Iseult, Pete Heintzman, Zoé Pochon, Toni de Dios Martínez, Raphael Eisenhofer, Claudio Ottoni, Åshild (Ash), Emrah Kırdök
🙌 Nikolay Oskolkov, Nasreen Broomand, James Fellows Yates, Pooja Swali, Pete Heintzman, Zoé Pochon, Claudio Ottoni
👍:skin_tone_3: Katerina Guschanski, Meriam van Os
👍:skin_tone_2: Meriam Guellil
👍:skin_tone_6: Miriam Bravo
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-05-31 06:40:07

Congrats @Antonio Fernandez-Guerra

https://elifesciences.org/articles/67667

eLife
Unifying the known and unknown microbial coding sequence space
A newly developed computational framework provides an overview of the extent, diversity, and relevance of the genes of unknown function in genomes and metagenomes.
Original URL: https://elifesciences.org/articles/67667
🎉 Nikolay Oskolkov, Eric Capo, Nico Rascovan
Nico Rascovan (nicorasco@gmail.com)
2022-05-31 17:32:37

*Thread Reply:* Congrats indeed Antonio!

👍 Antonio Fernandez-Guerra
Nico Rascovan (nicorasco@gmail.com)
2022-05-31 17:32:45

*Thread Reply:* looks super nice

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2022-05-31 07:03:45

Thanks @James Fellows Yates 😀 Check Chiara’s tweet thread for methodological aspects of the paper https://twitter.com/chiaravanni5/status/1531330691337789441

And Matt's for a more biological view https://twitter.com/mschecht_bio/status/1531329448003371009

twitter
} Chiara Vanni (https://twitter.com/ChiaraVanni5/status/1531330691337789441)
Our work on the dark side of genomes and metagenomes is finally out on <a href="https://twitter.com/eLife">@eLife</a>!! <https://elifesciences.org/articles/67667> Have a look at <a href="https://twitter.com/mschecht_bio">@mschecht_bio</a>'s thread for an overview of what AGNOSTOS unveils when analyzing genomic and metagenomic data. What is then AGNOSTOS? A 🧵 1/n
Original URL: https://twitter.com/chiaravanni5/status/1531330691337789441
Twitter
twitter
} Matthew S. Schechter (https://twitter.com/mschecht_bio/status/1531329448003371009)
Our work exploring microbial genes of unknown function is finally out in <a href="https://twitter.com/eLife">@eLife</a>! <https://doi.org/10.7554/eLife.67667> <a href="https://twitter.com/ChiaraVanni5">@ChiaraVanni5</a> Antonio Fernandez-Guerra <a href="https://twitter.com/tomodelmont">@tomodelmont</a> <a href="https://twitter.com/AcinasL">@AcinasL</a> <a href="https://twitter.com/merenbey">@merenbey</a> <a href="https://twitter.com/thesteinegger">@thesteinegger</a> <a href="https://twitter.com/carlosduartephd">@carlosduartephd</a> <a href="https://twitter.com/plbuttigieg">@plbuttigieg</a> <a href="https://twitter.com/el_pableras">@el_pableras</a> <a href="https://twitter.com/robdfinn">@robdfinn</a> et al. 1/n
Original URL: https://twitter.com/mschecht_bio/status/1531329448003371009
Twitter
👍 Nikolay Oskolkov, Nico Rascovan
Maxime Borry (maxime.borry@gmail.com)
2022-06-02 16:27:23

I talked about it last year in SPAAM3, and now it is published ! sam2lca is now officially released 🙂 https://joss.theoj.org/papers/10.21105/joss.04360 https://github.com/maxibor/sam2lca

Journal of Open Source Software
sam2lca: Lowest Common Ancestor for SAM/BAM/CRAM alignment files
Borry et al., (2022). sam2lca: Lowest Common Ancestor for SAM/BAM/CRAM alignment files. Journal of Open Source Software, 7(74), 4360, <https://doi.org/10.21105/joss.04360>
ISSN
2475-9066
Original URL: https://joss.theoj.org/papers/10.21105/joss.04360
GitHub
GitHub - maxibor/sam2lca: Lowest Common Ancestor from a SAM/BAM/CRAM alignment file
Lowest Common Ancestor from a SAM/BAM/CRAM alignment file - GitHub - maxibor/sam2lca: Lowest Common Ancestor from a SAM/BAM/CRAM alignment file
Original URL: https://github.com/maxibor/sam2lca
👍 Nikolay Oskolkov, Nico Rascovan
:mask_parrot: aidanva, Bjorn Bartholdy, Jasmin Frangenberg
👏 Maria Zicos, Christina Warinner
🤩 Christina Warinner
🙌 Mohamed Sarhan
Nikolay Oskolkov (nikolay.oskolkov@scilifelab.se)
2022-06-02 16:35:21

Cool, congratulations @Maxime Borry! What is now the output of sam2lca? I remember it was a jason while you were working on outputting a bam with multi-mappers assigned to higher taxonomic levels, is that implemented in this release?

Maxime Borry (maxime.borry@gmail.com)
2022-06-03 10:53:53

*Thread Reply:* https://sam2lca.readthedocs.io/en/latest/output.html 😉

👍 Nikolay Oskolkov
Nikolay Oskolkov (nikolay.oskolkov@scilifelab.se)
2022-06-03 11:56:17

*Thread Reply:* Awesome, thanks a lot @Maxime Borry, I am going to try it!

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-06-04 06:22:58

https://twitter.com/paleogenomics/status/1532933150141194240?t=vYNZPaLB2eX7MRDp04nsYg&s=19|https://twitter.com/paleogenomics/status/1532933150141194240?t=vYNZPaLB2eX7MRDp04nsYg&s=19

twitter
} paleogenomics (https://twitter.com/paleogenomics/status/1532933150141194240)
👀<a href="https://twitter.com/MiriamJBravo1">@MiriamJBravo1</a> <a href="https://twitter.com/MendozaArumi">@MendozaArumi</a> <https://twitter.com/StevenSalzberg1/status/1532734751282343937>
Original URL: https://twitter.com/paleogenomics/status/1532933150141194240?t=vYNZPaLB2eX7MRDp04nsYg&amp;s=19
Twitter
twitter
} Steven Salzberg 💙💛 (https://twitter.com/StevenSalzberg1/status/1532734751282343937)
Metagenomics folks: you no longer need a large-RAM computer to run Kraken! KrakenUniq has a new option that will automatically break your database into manageable pieces 1/2 <https://www.biorxiv.org/content/10.1101/2022.06.01.494344v1>
Twitter
👍 Nikolay Oskolkov, Zoé Pochon
🥳 Zoé Pochon, Ophélie Lebrasseur
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-06-09 11:10:59

New preprint from @Markella Moraitou @Adrian Forsythe and @Katerina Guschanski!

https://www.biorxiv.org/content/10.1101/2022.06.06.494923v1

"Dental calculus metagenomics suggest that ecology, not host phylogeny, shapes the oral microbiome in closely related species" - in ~19th/20th Gorilla dental calculus samples!

👍 Jasmin Frangenberg, Nikolay Oskolkov, Åshild (Ash), Sterling Wright
🎉 Åshild (Ash)
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-06-14 16:59:40

Not exactly a paper, but:

https://twitter.com/nfcore/status/1536615005084340225?t=wWkZ8ms4bkPp93eFQFj-tQ&s=19|https://twitter.com/nfcore/status/1536615005084340225?t=wWkZ8ms4bkPp93eFQFj-tQ&s=19

Reproducible, scalable, and portable De Novo assembly pipeline... Now with ancient DNA mode courtesy of @Maxime Borry and @Alex Hübner;)

twitter
} nf-core (https://twitter.com/nf_core/status/1536615005084340225)
Pipeline release! nf-core/mag v2.2.0 (Assembly and binning of metagenomes) See the changelog: <https://github.com/nf-core/mag/releases/tag/2.2.0>
Original URL: https://twitter.com/nf_core/status/1536615005084340225?t=wWkZ8ms4bkPp93eFQFj-tQ&amp;s=19
Twitter
👍 Nikolay Oskolkov, Åshild (Ash), Zoé Pochon
Alex Hübner (alexander_huebner@eva.mpg.de)
2022-06-14 16:59:42

@Alex Hübner has joined the channel

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-06-15 08:31:23

https://www.biorxiv.org/content/10.1101/2021.11.06.467582v3.abstract

bioRxiv
specificity: an R package for analysis of feature specificity to environmental and higher dimensional variables, applied to microbiome species data
Background: Understanding the factors that influence microbes' environmental distributions is important for determining drivers of microbial community composition. These include environmental variables like temperature and pH, and higher-dimensional variables like geographic distance and host species phylogeny. In microbial ecology, "specificity" is often described in the context of symbiotic or host parasitic interactions, but specificity can be more broadly used to describe the extent to which a species occupies a narrower range of an environmental variable than expected by chance. Using a standardization we describe here, Rao's (1982, 2010) Quadratic Entropy can be conveniently applied to calculate specificity of a feature, such as a species, to many different environmental variables. Results: We present our R package specificity for performing the above analyses, and apply it to four real-life microbial data sets to demonstrate its application. We found that many fungi within the leaves of native Hawaiian plants had strong specificity to rainfall and elevation, even though these variables showed minimal importance in a previous analysis of fungal beta-diversity. In Antarctic cryoconite holes, our tool revealed that many bacteria have specificity to co-occurring algal community composition. Similarly, in the human gut microbiome, many bacteria showed specificity to the composition of bile acids. Finally, our analysis of the Earth Microbiome Project data set showed that most bacteria show strong ontological specificity to sample type. Our software performed as expected on synthetic data as well. Conclusions: specificity is well-suited to analysis of microbiome data, both in synthetic test cases, and across multiple environment types and experimental designs. The analysis and software we present here can reveal patterns in microbial taxa that may not be evident from a community-level perspective. These insights can also be visualized and interactively shared among researchers using specificity 's companion package, specificity.shiny . ### Competing Interest Statement The authors have declared no competing interest.
Original URL: https://www.biorxiv.org/content/10.1101/2021.11.06.467582v3.abstract
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-06-15 08:31:40

I wonder if this would be useful for identifying true 'ancient' calculus, or just caluclus vs envirnomental stuff

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-06-15 08:32:25

(and this was the wrong slack channel, still applies though! )

👍 Nikolay Oskolkov
Maria Spyrou (spyrou@shh.mpg.de)
2022-06-15 13:25:42

https://www.nature.com/articles/s41598-022-13269-z

Nature
The human “contaminome”: bacterial, viral, and computational contamination in whole genome sequences from 1000 families
Scientific Reports - The human “contaminome”: bacterial, viral, and computational contamination in whole genome sequences from 1000 families
Original URL: https://www.nature.com/articles/s41598-022-13269-z
👍 Åshild (Ash), Nasreen Broomand, Nikolay Oskolkov
👍:skin_tone_2: Meriam Guellil
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-06-15 18:58:47

https://www.nature.com/articles/s41586-022-04800-3

Nature
The source of the Black Death in fourteenth-century central Eurasia
Nature - The source of the Black Death in fourteenth-century central Eurasia
Original URL: https://www.nature.com/articles/s41586-022-04800-3
Nico Rascovan (nicorasco@gmail.com)
2022-06-15 22:52:16

*Thread Reply:* Amazing! Great work Maria, congratulations!

Maria Spyrou (spyrou@shh.mpg.de)
2022-06-16 00:16:11

*Thread Reply:* Thank you!!

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-06-15 18:59:06

From @Maria Spyrou et al

👍 Nikolay Oskolkov, Sterling Wright, Nico Rascovan
👍:skin_tone_2: Meriam Guellil
:partyparrot: Åshild (Ash)
aidanva (aida.andrades@gmail.com)
2022-06-18 10:30:04

https://www.nature.com/articles/s42003-022-03527-1

Nature
A 16th century Escherichia coli draft genome associated with an opportunistic bile infection
Communications Biology - Ancient DNA from an Italian mummy’s gallstone provides insight into opportunistic E. coli infection.
Original URL: https://www.nature.com/articles/s42003-022-03527-1
👍:skin_tone_6: Miriam Bravo
👍 Alina Hiss, Åshild (Ash)
👍:skin_tone_2: Meriam Guellil
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-06-20 09:42:19

*Thread Reply:* good enough for paper of the week on twitter @aidanva?

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-06-20 12:46:48

*Thread Reply:* i'll schedule t for weds and you to give you time to change your mind

Maxime Borry (maxime.borry@gmail.com)
2022-06-18 22:23:10

I’ve been a bigger fan of Kraken2 so far (for its lower memory footprint and faster speed), but looks like KrakenUniq now has a nice point for itself ! https://www.biorxiv.org/content/10.1101/2022.06.01.494344v1

bioRxiv
Metagenomic classification with KrakenUniq on low-memory computers
Kraken and KrakenUniq are widely-used tools for classifying metagenomics sequences. A key requirement for these systems is a database containing all k-mers from all genomes that the users want to be able to detect, where k=31 by default. This database can be very large, easily exceeding 100 gigabytes (GB) and sometimes 400 GB. Previously, Kraken and KrakenUniq required loading the entire database into main memory (RAM), and if RAM was insufficient, they used memory mapping, which significantly increased the running time for large datasets. We have implemented a new algorithm in KrakenUniq that allows it to load and process the database in chunks, with only a modest increase in running time. This enhancement now makes it feasible to run KrakenUniq on very large datasets and huge databases on virtually any computer, even a laptop, while providing the same very high classification accuracy as the previous system. ### Competing Interest Statement The authors have declared no competing interest.
Original URL: https://www.biorxiv.org/content/10.1101/2022.06.01.494344v1
👀 James Fellows Yates
👍 Nikolay Oskolkov
👍:skin_tone_2: Meriam Guellil
Maxime Borry (maxime.borry@gmail.com)
2022-06-18 23:42:15

*Thread Reply:* That is, if you can build a DB for it

Nikolay Oskolkov (nikolay.oskolkov@scilifelab.se)
2022-06-20 08:01:49

*Thread Reply:* Yes, agree, potentially, a game changer. And a database can be shared. We have a nice collection of large databases for KrakenUniq

Maria Spyrou (spyrou@shh.mpg.de)
2022-06-21 09:59:18

https://www.nature.com/articles/s41564-022-01116-w

Nature
Ethical microbiome research with Indigenous communities
Nature Microbiology - Specific actions to develop equitable partnerships in microbiome research are proposed.
Original URL: https://www.nature.com/articles/s41564-022-01116-w
👍 James Fellows Yates, Bjorn Bartholdy
👀 James Fellows Yates
Marcel Keller (marcel.keller@ut.ee)
2022-07-02 10:25:38

https://www.biorxiv.org/content/10.1101/2022.06.30.498301v1

bioRxiv
Ancient Clostridium DNA and variants of tetanus neurotoxins associated with human archaeological remains
The analysis of microbial genomes from human archaeological samples offers a historic snapshot of ancient pathogens and provides insights into the origins of modern infectious diseases. Here, through large-scale metagenomic analysis of archeological samples, we discovered bacterial species related to modern-day Clostridium tetani, which produces tetanus neurotoxin (TeNT) and causes the disease tetanus. We were able to assemble 38 draft genomes from distinct human archeological samples spanning five continents from as early as ~4000 BCE. They display hallmarks of ancient DNA damage to variable degrees. While 20 fall into known C. tetani clades, phylogenetic analysis revealed novel C. tetani lineages, as well as a novel Clostridium species ("clade X") closely related to C. tetani. Within these genomes, we found 15 novel TeNT variants, including a unique lineage of TeNT found exclusively in ancient samples from South America. We experimentally produced and tested a TeNT variant selected from a ~6000-year-old Chilean mummy sample and found that it induced tetanus muscle paralysis in mice with extreme potency comparable to modern TeNT. Our work provides the first identification of neurotoxigenic C. tetani in ancient DNA, discovery of a new Clostridium species unique to ancient human samples, and a novel variant of tetanus neurotoxin that retains functional activity and ability to cause disease in mammals. ### Competing Interest Statement The authors have declared no competing interest.
Original URL: https://www.biorxiv.org/content/10.1101/2022.06.30.498301v1
👍:skin_tone_6: Miriam Bravo
🙌 Mohamed Sarhan
Nico Rascovan (nicorasco@gmail.com)
2022-07-18 16:57:28

nature.com/articles/s41598-022-10690-2

For the #ancientmetagenomedir ?

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-07-18 18:33:20

I don't think so, it doesn't look like they recover genomes

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-07-18 18:33:43

Also it's massively overamplieid (very stacky/duplicated) so I think it's unikely you could get there either sadly

👍 Nico Rascovan
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-07-25 14:43:18

(not ancient, but maybe partially relevant):

https://academic.oup.com/nar/article/50/13/e76/6583244

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-07-25 14:43:25

thoughts @Antonio Fernandez-Guerra?

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2022-07-25 14:49:56

yet another method based on consensus taxonomic classification of contigs in a MAG. Always is a good practice to run any of these methods to label potential problems

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2022-07-25 14:51:23

and of course, the microbial dark matter stuff: https://merenlab.org/2017/06/22/microbial-dark-matter/

Meren Lab
Microbial Dark Matter: The mullet of microbial ecology
It may sound cool today, but it will likely be a bit embarrassing to look back and see it in our history in about two decades from now.
Original URL: https://merenlab.org/2017/06/22/microbial-dark-matter/
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-07-25 14:51:44

*Thread Reply:* 😆

image.png
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-07-25 14:52:05

*Thread Reply:* Never fails to make me smile

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2022-07-25 14:53:07

*Thread Reply:* microbial marketing gone bad

😆 James Fellows Yates
Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2022-07-25 14:54:49

using mmseqs2 and their contig taxonomic workflow (https://academic.oup.com/bioinformatics/article/37/18/3029/6178277) you can get a similar output than what MDMcleaner is doing

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2022-07-25 14:58:03

I like this one https://github.com/dib-lab/charcoal

GitHub
GitHub - dib-lab/charcoal: Remove contaminated contigs from genomes using k-mers and taxonomies.
Remove contaminated contigs from genomes using k-mers and taxonomies. - GitHub - dib-lab/charcoal: Remove contaminated contigs from genomes using k-mers and taxonomies.
Original URL: https://github.com/dib-lab/charcoal
Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2022-07-25 14:59:02

although in all cases there are strong limitations when using taxonomic information

👍 James Fellows Yates
Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2022-07-25 15:01:02

we will be releasing soon some new methods to clean ancient assemblies and MAGs, will post it here when they are ready for others to use

👍 James Fellows Yates, Pete Heintzman
Alex Hübner (alexander_huebner@eva.mpg.de)
2022-07-25 15:16:49

I haven’t also been working on some sort of pipeline based on a two-step MMSeqs2 taxonomy approach to automatically remove potential wrongly binned and chimeric contigs. We have been using internally successfully for a couple of projects but it still needs more exploration and find tuning, I guess: https://github.com/alexhbnr/automatic_MAG_refinement I would like to know your thoughts on this, too, @Antonio Fernandez-Guerra! I was planning to contact you on this later this summer but will now take the opportunity! 🙂

GitHub
GitHub - alexhbnr/automatic_MAG_refinement
Contribute to alexhbnr/automatic_MAG_refinement development by creating an account on GitHub.
Original URL: https://github.com/alexhbnr/automatic_MAG_refinement
Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2022-07-25 15:58:06

Cool @Alex Hübner I will have a look and come back to you

👍 Alex Hübner
Åshild (Ash) (ashild.v@gmail.com)
2022-07-27 11:14:26

Congrats @Gunnar Neumann! “Ancient Yersinia pestis and Salmonella enterica genomes from Bronze Age Crete” https://www.sciencedirect.com/science/article/pii/S0960982222011010?via%3Dihub

sciencedirect.com
Ancient Yersinia pestis and Salmonella enterica genomes from Bronze Age Crete
During the late 3rd millennium BCE, the Eastern Mediterranean and Near East witnessed societal changes in many regions, which are usually explained wi…
Original URL: https://www.sciencedirect.com/science/article/pii/S0960982222011010?via%3Dihub
🎉 Maria Zicos, James Fellows Yates, irinavelsko, Alina Hiss, Pooja Swali, Anna F., Bjorn Bartholdy, Maria Spyrou, Hannah Moots, Marcel Keller
👏 James Fellows Yates, Nikolay Oskolkov, Nico Rascovan, Christina Warinner, Ophélie Lebrasseur, Hannah Moots
👏:skin_tone_2: Meriam Guellil
:mask_parrot: aidanva
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-07-28 15:24:45

And congrats to @Meriam Guellil!

😀 Meriam Guellil
👍 Nikolay Oskolkov, Maria Spyrou
🎉 Christina Warinner, Åshild (Ash), Marcel Keller
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-07-28 15:24:46

https://www.science.org/doi/10.1126/sciadv.abo4435

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-08-16 09:07:27

Congrats to @Vilma Perez (or @Vilma Pérez ?)

https://www.mdpi.com/2076-2607/10/8/1623

MDPI
A Case Study for the Recovery of Authentic Microbial Ancient DNA from Soil Samples
High Throughput DNA Sequencing (HTS) revolutionized the field of paleomicrobiology, leading to an explosive growth of microbial ancient DNA (aDNA) studies, especially from environmental samples. However, aDNA studies that examine environmental microbes routinely fail to authenticate aDNA, examine laboratory and environmental contamination, and control for biases introduced during sample processing. Here, we surveyed the available literature for environmental aDNA projects&amp;mdash;from sample collection to data analysis&amp;mdash;and assessed previous methodologies and approaches used in the published microbial aDNA studies. We then integrated these concepts into a case study, using shotgun metagenomics to examine methodological, technical, and analytical biases during an environmental aDNA study of soil microbes. Specifically, we compared the impact of five DNA extraction methods and eight bioinformatic pipelines on the recovery of microbial aDNA information in soil cores from extreme environments. Our results show that silica-based methods optimized for aDNA research recovered significantly more damaged and shorter reads (&lt;100 bp) than a commercial kit or a phenol&amp;ndash;chloroform method. Additionally, we described a stringent pipeline for data preprocessing, efficiently decreasing the representation of low-complexity and duplicated reads in our datasets and downstream analyses, reducing analytical biases in taxonomic classification.
Original URL: https://www.mdpi.com/2076-2607/10/8/1623
👍 Nikolay Oskolkov, Jasmin Frangenberg, Sterling Wright
🎉 Gunnar Neumann, Miriam Bravo, Vilma Pérez
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-08-16 09:07:43

*Thread Reply:* Do you want the SPAAM twitter to tweet it @Vilma Pérez /@Vilma Perez?

Vilma Pérez (vilma.bq@gmail.com)
2022-10-20 06:05:34

*Thread Reply:* hey @James Fellows Yates I opened slack after many many months, apologies I didn’t your messages before!.

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-10-20 06:16:28

*Thread Reply:* No worries!

Vilma Perez (vilma.perez@adelaide.edu.au)
2022-08-16 09:07:29

@Vilma Perez has joined the channel

Vilma Pérez (vilma.bq@gmail.com)
2022-08-16 09:07:29

@Vilma Pérez has joined the channel

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-09-02 19:23:03

https://doi.org/10.1093/pnasnexus/pgac148

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-09-02 19:23:12

From @irinavelsko!

🙌 Bjorn Bartholdy, Raphael Eisenhofer, Nikolay Oskolkov, Mohamed Sarhan, Sterling Wright, Jasmin Frangenberg, Christina Warinner, Percy Ho, I-Ting Huang
🎉 Åshild (Ash), Katerina Guschanski, Jasmin Frangenberg, Christina Warinner, I-Ting Huang
👍 irinavelsko
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-09-26 19:57:48

Congrats to @Jessica Hider who is somehow publishing from the future 🤔

https://www.sciencedirect.com/science/article/pii/S1879981722000420?dgcid=coauthor

sciencedirect.com
Examining pathogen DNA recovery across the remains of a 14th century Italian friar (Blessed Sante) infected with Brucella melitensis
To investigate variation in ancient DNA recovery of Brucella melitensis, the causative agent of brucellosis, from multiple tissues belonging to one in…
Original URL: https://www.sciencedirect.com/science/article/pii/S1879981722000420?dgcid=coauthor
👏:skin_tone_3: Katerina Guschanski
👏 Nikolay Oskolkov, Hannah Moots, irinavelsko, Iseult, Gunnar Neumann, aidanva, Alina Hiss, Åshild (Ash)
👏:skin_tone_6: Miriam Bravo
👏:skin_tone_2: Meriam Guellil, Kelly Blevins
😁 Jessica Hider
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-09-26 19:57:58

"Examining pathogen DNA recovery across the remains of a 14th century Italian friar (Blessed Sante) infected with Brucella melitensis"

Jessica Hider (hiderj@mcmaster.ca)
2022-11-09 20:26:51

*Thread Reply:* Thanks @James Fellows Yates :partyparrot: (sorry, I'm slacking off on my slack lol). I'm also confused about my future publishing, very impressive of me lol.

😆 James Fellows Yates
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-10-02 07:27:55

https://www.sciencedirect.com/science/article/pii/S0960982222014671

Not metagenomics but very closely related:

Also including @Åshild (Ash) @Anna F. (And likely a bunch of others sorry, too long author list)

sciencedirect.com
The population genomic legacy of the second plague pandemic
Human populations have been shaped by catastrophes that may have left long-lasting signatures in their genomes. One notable example is the second plag…
Original URL: https://www.sciencedirect.com/science/article/pii/S0960982222014671
👍:skin_tone_6: Miriam Bravo
👍 Sterling Wright, Davide Bozzi, Christina Warinner
Nico Rascovan (nicorasco@gmail.com)
2022-10-03 19:07:02

https://www.nature.com/articles/s41596-022-00738-y

I think this is a useful one for many here, mostly those that are just jumping into the ancient metagenomics stuff

Nature
Metagenome analysis using the Kraken software suite
Nature Protocols - The authors provide a guide to using the Kraken suite for metagenomics analysis, including classification, quantification and visualization, illustrated by quantification of...
Original URL: https://www.nature.com/articles/s41596-022-00738-y
👍 Anna Chagas, Nikolay Oskolkov, Louis Lhote, Bjorn Bartholdy, Ivany Argueta
👍:skin_tone_2: Kelly Blevins
👍:skin_tone_6: Miriam Bravo
💯 Kadir Toykan Özdoğan
👍:skin_tone_3: Meriam van Os
💡 Jean-Luc Tison
Nico Rascovan (nicorasco@gmail.com)
2022-10-04 09:43:27

https://www.nature.com/articles/s41598-022-20193-9

Another one for the AncientMetagenomeDir

Nature
Changes in the oral status and periodontal pathogens in a Sardinian rural community from pre-industrial to modern time
Scientific Reports - Changes in the oral status and periodontal pathogens in a Sardinian rural community from pre-industrial to modern time
Original URL: https://www.nature.com/articles/s41598-022-20193-9
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-10-04 09:52:32

That's just RT-PCR no?

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-10-04 09:52:53

Oh and 16S, but it needs to e shotgun 😉

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-10-04 09:53:03

Also:

image.png
😫 Bjorn Bartholdy
😶 Katerina Guschanski
:slam: Åshild (Ash)
🥴 Miriam Bravo
🫢 Raphael Eisenhofer
👎:skin_tone_2: Kelly Blevins
Åshild (Ash) (ashild.v@gmail.com)
2022-10-04 15:07:32

*Thread Reply:* How is that possible?! Scientific Reports is a Nature publication, don’t they require you put the data online?

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-10-04 15:44:55

*Thread Reply:* 😬

Raphael Eisenhofer (raph.eisenhofer@gmail.com)
2022-10-04 22:41:26

*Thread Reply:* They require you to pay them money 💰

💸 James Fellows Yates
Nico Rascovan (nicorasco@gmail.com)
2022-10-04 09:58:38

haaha, ok, my bad, I didn’t see all that… I just read the title and very quickly the abstract and asumed it was shotgun

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-10-06 08:27:55

In much better news:

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-10-06 08:27:56

https://www.biorxiv.org/content/10.1101/2022.10.03.510579v1

bioRxiv
aMeta: an accurate and memory-efficient ancient Metagenomic profiling workflow
Analysis of microbial data from archaeological samples is a rapidly growing field with a great potential for understanding ancient environments, lifestyles and disease spread in the past. However, high error rates have been a long-standing challenge in ancient metagenomics analysis. This is also complicated by a limited choice of ancient microbiome specific computational frameworks that meet the growing computational demands of the field. Here, we propose aMeta, an accurate ancient Metagenomic profiling workflow designed primarily to minimize the amount of false discoveries and computer memory requirements. Using simulated ancient metagenomic samples, we benchmark aMeta against a current state-of-the-art workflow, and demonstrate its superior sensitivity and specificity in both microbial detection and authentication, as well as substantially lower usage of computer memory. aMeta is implemented as a Snakemake workflow to facilitate use and reproducibility. ### Competing Interest Statement The authors have declared no competing interest.
Original URL: https://www.biorxiv.org/content/10.1101/2022.10.03.510579v1
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-10-06 08:29:21

"aMeta: an accurate and memory-efficient ancient Metagenomic profiling workflow"

From @Zoé Pochon @Nora Bergfeldt @Emrah Kırdök @Tom van der Valk @Nikolay Oskolkov and co!

(I guess you'll need to update your #SPAAM4 title @Nikolay Oskolkov 😉 )

". Here, we propose aMeta, an accurate ancient Metagenomic profiling workflow designed primarily to minimize the amount of false discoveries and computer memory requirements."

🎉 Nora Bergfeldt, Maria Spyrou, Åshild (Ash), Shreya, Hannah Moots, Biancamaria Bonucci
🙏 Nikolay Oskolkov
🥳 Zoé Pochon
👏 Kadir Toykan Özdoğan, Pete Heintzman, Maria Spyrou
🙌:skin_tone_3: Meriam van Os
Nikolay Oskolkov (nikolay.oskolkov@scilifelab.se)
2022-10-06 08:44:04

*Thread Reply:* Thank you James! I have already let @Shreya know the new title of the talk at SPAAM4 🙂

:catjam: James Fellows Yates
:partyparrot: Shreya
Zoé Pochon (zoe.pochon@gmail.com)
2022-10-06 08:48:17

*Thread Reply:* Thanks! I hope people will find the pipeline useful 😊 (I pushed for a shorter name for it, mea culpa 😅)

👍 Nikolay Oskolkov, Davide Bozzi
Nora Bergfeldt (nora.bergfeldt@gmail.com)
2022-10-06 08:51:42

*Thread Reply:* @Zoé Pochon i still think MEAD would have been funnier 😅 😉 😘

😂 Zoé Pochon, Nikolay Oskolkov, Shreya
👍 Zoé Pochon, Nikolay Oskolkov
💯 James Fellows Yates, Nikolay Oskolkov
Nico Rascovan (nicorasco@gmail.com)
2022-10-06 09:05:49

*Thread Reply:* Great that is already out! I was waiting for it @Nikolay Oskolkov! Looking forward to test it!

👍 Nikolay Oskolkov
Nico Rascovan (nicorasco@gmail.com)
2022-10-06 09:06:41

*Thread Reply:* Are the DBs already available for downloading?

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-10-06 09:06:59

*Thread Reply:* @Nico Rascovan dude up your twitter game, @Nikolay Oskolkov tweeted that couple of days ago 😉

Emrah Kırdök (emrahkirdok@gmail.com)
2022-10-06 09:07:15

*Thread Reply:* Thank you @James Fellows Yates and thanks to the co authors @Zoé Pochon @Nora Bergfeldt @Nikolay Oskolkov @Tom van der Valk for this great work!

:catjam: James Fellows Yates
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-10-06 09:07:30

*Thread Reply:* https://twitter.com/NikolayOskolkov/status/1575009604437561345

twitter
} Nikolay Oskolkov (https://twitter.com/NikolayOskolkov/status/1575009604437561345)
We make a few large KrakenUniq databases and Bowtie2 indexes public. We used them for metagenomic profiling of aDNA samples in the upcoming publication. Great collaboration with <a href="https://twitter.com/AndersGother">@AndersGother</a> <a href="https://twitter.com/ZoePochon">@ZoePochon</a> <a href="https://twitter.com/nora_bergfeldt">@nora_bergfeldt</a> Emrah Kirdök <a href="https://twitter.com/unnebe">@unnebe</a> Claudio Mirabello <a href="https://twitter.com/SciLifeLab_DC">@SciLifeLab_DC</a> <a href="https://twitter.com/NBISwe">@NBISwe</a> <https://twitter.com/scilifelab_dc/status/1572106511534686208>
Original URL: https://twitter.com/NikolayOskolkov/status/1575009604437561345
Twitter
twitter
} SciLifeLab_DataCentre (https://twitter.com/SciLifeLab_DC/status/1572106511534686208)
Check out the latest <b>#opendata</b> items published in the <a href="https://twitter.com/scilifelab">@scilifelab</a> Data Repository! Bowtie2 index for full NCBI NT database (<https://doi.org/10.17044/scilifelab.21070063>) &amp; KrakenUniq database based on microbial part of NCBI NT (<https://doi.org/10.17044/scilifelab.2051825>) #OpenScience <a href="https://twitter.com/KAWstiftelsen">@KAWstiftelsen</a>
Twitter
Nikolay Oskolkov (nikolay.oskolkov@scilifelab.se)
2022-10-06 09:07:33

*Thread Reply:* Yes @Nico Rascovan, the links are mentioned in the preprint, but I am also going to post them in the "general" channel, hope they will be of interest for many people

🙌 Nico Rascovan, Åshild (Ash)
Nico Rascovan (nicorasco@gmail.com)
2022-10-06 09:07:38

*Thread Reply:* hahaha, I barely check twitter…. If it does not send me a notification to my phone, I won’t see it

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-10-06 09:07:53

*Thread Reply:* shakes head

Nico Rascovan (nicorasco@gmail.com)
2022-10-06 09:11:14

*Thread Reply:* re-twitted!

Nico Rascovan (nicorasco@gmail.com)
2022-10-06 09:12:33

*Thread Reply:* @Nikolay Oskolkov Do you have the full NCBI DB indexed for KrakenUniq? I think Eukaryotic reads are highly underexplored

Nikolay Oskolkov (nikolay.oskolkov@scilifelab.se)
2022-10-06 09:24:40

*Thread Reply:* Thank you @Nico Rascovan for re-twitting! 🙏 The full NCBI NT is available here KrakenUniq database based on full NCBI NT: <https://doi.org/10.17044/scilifelab.20205504>

Nikolay Oskolkov (nikolay.oskolkov@scilifelab.se)
2022-10-06 09:36:13

*Thread Reply:* @Nico Rascovan this database contains both eukaryotic and prokaryotic references. However, while prokaryotic references are often complete genomes or chromosome level assemblies, the eukaryotic references are usually of a bad quality, so only pieces of reference genomes. This has advantages and disadvantages. The advantage is that the DB is possible to fit to the RAM and that the eukaryotic references can be used as a decoy to attract potential eukaryotic contamination. The disadvantage is that the varying quality of eukaryotic references creates a "database bias", i.e. when one discovers e.g. a wolf in a metagenomic sample just because wolf happened to have a better quality reference (included into NT) compared to the reference of bison that is truly present in the sample

Nico Rascovan (nicorasco@gmail.com)
2022-10-06 09:48:21

*Thread Reply:* Yes, I totally see the point. But including any known sequence (at least any sequence in the NCBI nt db) would allow reducing a bit the high percentage of unclassified reads you get with KrakenUniq. Then, as you mention and shown already before, there are downstream analyses that can be done to further authenticate, characterize or understand what do certain hits mean. No kraken results should be taken for granted without some controls.

👍 Nikolay Oskolkov, Zoé Pochon
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-10-06 09:38:21

Oh man, you guuys are on a roll https://www.nature.com/articles/s41467-022-33494-4#Sec11

Congrats to @Linda Armbrecht and team!

Nature
Ancient marine sediment DNA reveals diatom transition in Antarctica
Nature Communications - Sedimentary ancient DNA can indicate ecosystem-wide changes. Here, the authors show association between warm phases and high diatom abundance in the Antarctic Scotia Sea, in...
Original URL: https://www.nature.com/articles/s41467-022-33494-4#Sec11
🎉 Nikolay Oskolkov, Pete Heintzman
👍 Åshild (Ash)
❤️ Eric Capo
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-10-06 09:40:02

And @Rita M Austin https://www.nature.com/articles/s42003-022-03890-z

Nature
Remembering St. Louis individual—structural violence and acute bacterial infections in a historical anatomical collection
Communications Biology - An investigation into the cause of death of St. Louis Individual, a 23-year old Black or African American male who died in the 1930s, reveals evidence of structural...
Original URL: https://www.nature.com/articles/s42003-022-03890-z
👍 Nikolay Oskolkov
❤️ Rita M Austin
🎉 Åshild (Ash), Cameron Pauly, Pooja Swali
Rita M Austin (rita.austin@nhm.uio.no)
2022-10-06 09:40:05

@Rita M Austin has joined the channel

Shreya (shreya23@uchicago.edu)
2022-10-19 19:33:25

https://www.nature.com/articles/s41586-022-05349-x Cool paper out by SPAAM4 career panelist Jennifer Klunk!

Nature
Evolution of immune genes is associated with the Black Death
Nature - Klunk and colleagues identify signatures of natural selection imposed by Yersinia pestis and demonstrate their effect on genetic diversity and susceptibility to certain diseases in the...
Original URL: https://www.nature.com/articles/s41586-022-05349-x
:mask_parrot: Alex Hübner, Pete Heintzman
🙌 Sterling Wright, Constanza de la Fuente, Anna F., Nikolay Oskolkov, Åshild (Ash)
🦠 Miriam Bravo
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-10-24 09:47:04

Not metagenomics, but possibly of interest to those working on eDNA metacoding data: https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.13356

Åshild (Ash) (ashild.v@gmail.com)
2022-10-31 13:09:26

Paper and blog post about FAIR principles for research software:

Nature campaign=relatedcontent&utmsource=RSDT&utmmedium=Communities|Introducing the FAIR Principles for research software> Scientific Data - Introducing the FAIR Principles for research software https://researchdata.springernature.com/posts/introducing-the-fair-principles-for-research-software?utmsource=newslettermailer&utmmedium=email&utmcampaign=newsletter|https://researchdata.springernature.com/posts/introducing-the-fair-principles-for-research-s[…]ettermailer&utmmedium=email&utm_campaign=newsletter

Research Data at Springer Nature source=newslettermailer&utmmedium=email&utmcampaign=newsletter|Introducing the FAIR Principles for research software>

Nature
Introducing the FAIR Principles for research software
Scientific Data - Introducing the FAIR Principles for research software
Original URL: https://www.nature.com/articles/s41597-022-01710-x?utm_campaign=related_content&amp;utm_source=RSDT&amp;utm_medium=Communities
Research Data at Springer Nature
Introducing the FAIR Principles for research software
Original URL: https://researchdata.springernature.com/posts/introducing-the-fair-principles-for-research-software?utm_source=newsletter_mailer&amp;utm_medium=email&amp;utm_campaign=newsletter
🙌 Jasmin Frangenberg, Biancamaria Bonucci
👍:skin_tone_6: Miriam Bravo
👍 Alex Hübner
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-11-22 08:43:31

https://www.nature.com/articles/s42003-022-04190-2

Nature
Genomic ancestry, diet and microbiomes of Upper Palaeolithic hunter-gatherers from San Teodoro cave
Communications Biology - A combined ancient genomic, metagenomic, and paleoproteomic analysis reveals lifestyle and dietary information of Upper Palaeolithic huntergatherers from San Teodoro cave...
Original URL: https://www.nature.com/articles/s42003-022-04190-2
👍 Nikolay Oskolkov, Cameron Pauly, Sterling Wright, Sarah Johnson
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-11-23 10:34:04

https://www.nature.com/articles/s41467-022-34416-0

Nature
Ancient oral microbiomes support gradual Neolithic dietary shifts towards agriculture
Nature Communications - Here, the authors compare 76 dental calculus oral microbiomes from Palaeolithic hunter-gatherers with Neolithic and Copper Age farmers living in the same region of Italy....
Original URL: https://www.nature.com/articles/s41467-022-34416-0
Nico Rascovan (nicorasco@gmail.com)
2022-11-23 10:39:20

*Thread Reply:* I think this is a paper that worth discussing in the SPAAM community, as they implemented some new strategies to analyze ancient microbiome data, that have not been used before in the field.

👍 Nikolay Oskolkov, Biancamaria Bonucci, Cameron Pauly
Nico Rascovan (nicorasco@gmail.com)
2022-11-23 10:40:20

*Thread Reply:* Maybe @Andrea quagliariello can make a summary about it for the rest of the community, I think it will be very useful for others

👍 Nikolay Oskolkov, Biancamaria Bonucci, Andrea quagliariello, Cameron Pauly
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-11-23 10:52:05

*Thread Reply:* #spaamtisch?

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-11-23 10:52:09

*Thread Reply:* (@Maria Lopopolo)

Maria Lopopolo (maria.lopopolo1989@gmail.com)
2022-11-23 11:16:05

*Thread Reply:* I can definitely propose it to the community among the topics as broad discussion although this is more JC material. But well in our first #spaamtisch we'll see what people think the channel should be dedicated to ;)

❤️ Biancamaria Bonucci
Andrea quagliariello (quagliariello.andrea@gmail.com)
2022-11-23 12:03:20

*Thread Reply:* Thank you @Nico Rascovan yes I would be delighted to do that for the community!!! But you have to wait some days because, unfortunately, I am sick at home with flu 🥲. Thus, instead of going out with my collegues to celebrate it, I am at home with the blanket and the hot water bottle:mask_parrot:🤣. I promise I will come back soon🙏💪

🤒 James Fellows Yates, Biancamaria Bonucci
💪 Nico Rascovan, Cameron Pauly, Claudio Ottoni
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-11-23 13:07:20

*Thread Reply:* Get well soon!

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-11-24 09:15:15

*Thread Reply:* OK it would be coolto have an open discussion, I already have questions!

Claudio Ottoni (claudio.ottoni@uniroma2.it)
2022-11-24 11:13:58

*Thread Reply:* Great study @Andrea quagliariello congratulations!

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-11-23 10:34:08

Ancient oral microbiomes support gradual Neolithic dietary shifts towards agriculture

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-11-23 10:34:50

Congrats to @Andrea quagliariello!

👍 Nikolay Oskolkov, Nico Rascovan, Maria Lopopolo
🥳 Gunnar Neumann
👏 Claudio Ottoni
Andrea quagliariello (quagliariello.andrea@gmail.com)
2022-11-23 12:04:49

*Thread Reply:* Thank you @James Fellows Yates!!!🙂

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-11-24 09:12:17

*Thread Reply:* Btw ❤️ for citing protocols.io protocols 😄

Andrea quagliariello (quagliariello.andrea@gmail.com)
2022-11-24 11:52:47

*Thread Reply:* 😄of course!!! 🙂

Nico Rascovan (nicorasco@gmail.com)
2022-11-23 10:40:42

It is a very nice article! 🎉👏

👍 Nikolay Oskolkov, Cameron Pauly
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-11-24 09:37:01

You can tell it's coming to the end of the year 😆

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-11-24 09:37:04

https://www.biorxiv.org/content/10.1101/2022.01.27.477466v1.full

bioRxiv
Indigenous peoples in eastern Brazil: insights from 19th century genomes and metagenomes
Although Brazil was inhabited by more than 3,000 Indigenous populations prior to European colonization, today’s Indigenous peoples represent less than 1% of Brazil’s census population. Some of the decimated communities belonged to the so-called “Botocudos” from central-eastern Brazil. These peoples are thought to represent a case of long-standing genetic continuity bearing a strong craniometric resemblance to that of the oldest Indigenous Americans (“Paleoamericans”). Yet, little is known about their origins and genetic relationship to other Native Americans, as only two “Botocudo” genomes have been sequenced so far and those were surprisingly of Polynesian ancestry. To deepen our knowledge on the genomic history of pre-contact Indigenous Americans and the pathogens they were exposed to, we carbon-dated and sequenced 24 ancient Brazilians (including 22 “Botocudos”) whose remains were hosted at the National Museum of Rio de Janeiro and recovered prior to the tragic 2018 fire. The resulting genomes’ depth of coverage ranged from 0.001× to 24×. Their genetic ancestry was found to be Indigenous American without gene flow from external populations such as Europeans, Africans or Polynesians. Unlike Mesoamericans, the “Botocudos” and Amazonians do not seem to have experienced a population expansion once in the Americas. Moreover, remarkably, their genomes exhibit amongst the lowest levels of heterozygosity worldwide and long runs of homozygosity, which could be explained by unique social practices or a very small effective size. Finally, whole genomes of likely ancient pathogens were recovered, including lineages of Human parvovirus B19 that were possibly introduced after the European contact. Significance statement To better understand the genetic relationship among Indigenous populations in Brazil, we sequenced the genomes of 24 ancient individuals (22 of which labelled as “Botocudos”, a term used to describe hunter-gatherer tribes) whose remains were hosted at the Museu Nacional of Rio de Janeiro prior to the tragic fire that consumed it in 2018. Unlike two previously published “Botocudo” genomes, the 22 “Botocudos” from this study have Indigenous American-related ancestry without any Polynesian-related ancestry, and they are similarly related to several Native Brazilian populations. Finally, unlike Eurasian hunter-gatherers, the “Botocudos” exhibit among the lowest heterozygosity and longest runs of homozygosity worldwide – compatible with a very small effective size and suggesting a unique social structure among hunter-gatherers in the Americas. ### Competing Interest Statement The authors have declared no competing interest.
Original URL: https://www.biorxiv.org/content/10.1101/2022.01.27.477466v1.full
:catjam: Davide Bozzi, Maria Lopopolo, Miriam Bravo
🙌 Constanza de la Fuente, Sterling Wright, Zoé Pochon
👍:skin_tone_3: Meriam van Os
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-11-24 09:37:32

From @Diana Ivette Cruz Dávalos @Miriam Bravo @Samuel Neuenschwander @Viridiana Villa and co!

Sarah Johnson (sarahjjohnson@ou.edu)
2022-12-02 17:32:26

Jacob Haffner here at LMAMR published this awesome paper on the human metabolome!

Untargeted Fecal Metabolomic Analyses across an Industrialization Gradient Reveal Shared Metabolites and Impact of Industrialization on Fecal Microbiome-Metabolome Interactions https://journals.asm.org/doi/full/10.1128/msystems.00710-22

👍 Nikolay Oskolkov, Sterling Wright
☝️ James Fellows Yates
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-12-05 16:23:48

https://academic.oup.com/nargab/article/4/4/lqac090/6855701

👍 irinavelsko, Nikolay Oskolkov, Alex Hübner, Jasmin Frangenberg
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-12-05 16:24:17

*Thread Reply:* @Alex Hübner @irinavelsko

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-12-05 16:24:07

> *Comparison of functional classification systems * > In microbiome analysis, functional profiling is based on assigning reads or contigs to terms or nodes in a functional classification system. There are a number of large, general-purpose functional classifications that are in use, such as eggNOG, KEGG, InterPro and SEED. Smaller, special-purpose classifications include CARD, EC, MetaCyc and VFDB. Here, we compare the different classifications in terms of their overlap, redundancy, structure and assignment rates. We also provide mappings between main concepts in different classifications. For the large classifications, we find that eggNOG performs the best with respect to sequence redundancy and structure, SEED has the cleanest hierarchy, whereas KEGG and InterPro:BP might be more informative for medical applications. We illustrate the practical assignment rates for different classifications using a number of metagenomic samples

Nico Rascovan (nicorasco@gmail.com)
2022-12-07 18:05:23

https://www.nature.com/articles/s41586-022-05453-y

2-Million years old sedaDNA! Impressive! Congrats @Antonio Fernandez-Guerra that participated in the work and presented some exciting results of the study in our institute last week!

Nature
A 2-million-year-old ecosystem in Greenland uncovered by environmental DNA
Nature - Analysis of two-million-year-old ancient environmental DNA from the Kap København Formation in North Greenland shows there was an open boreal forest with diverse plant and animal...
Original URL: https://www.nature.com/articles/s41586-022-05453-y
👏 James Fellows Yates, Zandra Fagernäs, irinavelsko, Camila Duitama, Pete Heintzman, Miki Bálint
👏:skin_tone_2: Meriam Guellil
🤯 Kadir Toykan Özdoğan, Miriam Bravo, Constanza de la Fuente, Nikolay Oskolkov
🎉 Åshild (Ash), Kelly Blevins
Nikolay Oskolkov (nikolay.oskolkov@scilifelab.se)
2022-12-08 13:00:30

*Thread Reply:* the race has begun 🙂

Maxime Borry (maxime.borry@gmail.com)
2022-12-09 11:56:22

*Thread Reply:* Race to finding the oldest DNA again ? Back to amber ?

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-12-07 18:09:57

And also to @Markella Moraitou @Adrian Forsythe @Jaelle Brealey @Katerina Guschanski

https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msac263/6874787?utmsource=advanceaccess&utmcampaign=mbe&utmmedium=email|https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msac263/6874787?utmsource=advanceaccess&utmcampaign=mbe&utmmedium=email

🎉 Meriam Guellil, Miriam Bravo, irinavelsko, Camila Duitama, Åshild (Ash), Nikolay Oskolkov, Maria Lopopolo, Kelly Blevins, Miki Bálint
Markella Moraitou (Markella.Moraitou.0437@student.uu.se)
2022-12-07 18:10:01

@Markella Moraitou has joined the channel

Adrian Forsythe (adrian.forsythe@ebc.uu.se)
2022-12-07 18:10:01

@Adrian Forsythe has joined the channel

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-12-08 21:29:28

MEGAN-Server... Is back...?

https://www.biorxiv.org/content/10.1101/2022.12.05.518498v1?rss=1

bioRxiv
Megan Server: facilitating interactive access to metagenomic data on a server
Motivation: Metagenomic projects of large sequencing datasets (totaling hundreds of gigabytes of data). Thus, computational preprocessing and analysis are usually performed on a server rather than on a personal computer. The results of such analyses are then usually explored interactively. One approach is to use MEGAN, an interactive program that allows analysis and comparison of metagenomic datasets. Previous releases of MEGAN have required that the user first download the computed data from the server, an increasingly time-consuming process. Here we present Megan Server, a stand-alone program that serves MEGAN files to the web, using a RESTful API, facilitating interactive analysis without downloading the complete data. We describe a number of different application scenarios. Availability: Megan Server is provided as a standalone program tools/megan-server in the Megan6 software suite, available at <https://software-ab.cs.uni-tuebingen.de/> download/megan6. ### Competing Interest Statement The authors have declared no competing interest.
Original URL: https://www.biorxiv.org/content/10.1101/2022.12.05.518498v1?rss=1
👍 Nikolay Oskolkov
👀 Bjorn Bartholdy
Åshild (Ash) (ashild.v@gmail.com)
2022-12-10 17:46:28

*Thread Reply:* Was it ever gone? Haven’t used it since 2017 I think

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-12-10 17:53:45

*Thread Reply:* As in it stopped being developed

👍 Åshild (Ash)
Cameron Pauly (cjpauly3@gmail.com)
2022-12-12 21:30:00

https://doi.org/10.1111/omi.12404

Cameron Pauly (cjpauly3@gmail.com)
2022-12-12 21:32:14

Congratulations @Andrea quagliariello !!

👏 James Fellows Yates, irinavelsko, Nikolay Oskolkov
👍 Gabriel Innocenti
Cameron Pauly (cjpauly3@gmail.com)
2022-12-12 21:37:01

But my institution doesn't pay for access to the journal so I can't read it 😭😭

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-12-13 09:00:41
Molecular Oral Microbiology - 2022 - Innocenti - Dental calculus microbiome correlates with dietary intake.pdf
👍 Nikolay Oskolkov, Gabriel Innocenti
😍 Cameron Pauly
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-12-13 09:01:44

(hope that's OK @Andrea quagliariello!)

Andrea quagliariello (quagliariello.andrea@gmail.com)
2022-12-13 10:16:39

*Thread Reply:* Absolutely yes!! thank you @James Fellows Yates Also because I requested to make it open access

Joanna H. Bonczarowska (j.bonczarowska@ikmb.uni-kiel.de)
2022-12-13 09:13:22

https://doi.org/10.1186/s13059-022-02806-8

BioMed Central
Pathogen genomics study of an early medieval community in Germany reveals extensive co-infections - Genome Biology
Background The pathogen landscape in the Early European Middle Ages remains largely unexplored. Here, we perform a systematic pathogen screening of the rural community Lauchheim “Mittelhofen,” in present-day Germany, dated to the Merovingian period, between fifth and eighth century CE. Skeletal remains of individuals were subjected to an ancient DNA metagenomic analysis. Genomes of the detected pathogens were reconstructed and analyzed phylogenetically. Results Over 30% of the individuals exhibit molecular signs of infection with hepatitis B virus (HBV), parvovirus B19, variola virus (VARV), and Mycobacterium leprae. Seven double and one triple infection were detected. We reconstructed four HBV genomes and one genome each of B19, VARV, and M. leprae. All HBV genomes are of genotype D4 which is rare in Europe today. The VARV strain exhibits a unique pattern of gene loss indicating that viruses with different gene compositions were circulating in the Early Middle Ages. The M. leprae strain clustered in branch 3 together with the oldest to-date genome from the UK. Conclusions The high burden of infectious disease, together with osteological markers of physiological stress, reflect a poor health status of the community. This could have been an indirect result of the climate decline in Europe at the time, caused by the Late Antique Little Ice Age (LALIA). Our findings suggest that LALIA may have created an ecological context in which persistent outbreaks set the stage for major epidemics of severe diseases such as leprosy and smallpox hundreds of years later.
Original URL: https://doi.org/10.1186/s13059-022-02806-8
👀 James Fellows Yates
👍 Nikolay Oskolkov, Åshild (Ash)
😍 Andrea quagliariello
👍:skin_tone_2: Meriam Guellil
🎉 Gunnar Neumann
🙌:skin_tone_3: Meriam van Os
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-12-13 09:14:59

*Thread Reply:* Congrats @Joanna H. Bonczarowska!

❤️ Joanna H. Bonczarowska
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-12-13 09:17:46

*Thread Reply:* Would you be interesting in adding the genomes to AncientMetagenomeDir? https://github.com/SPAAM-community/AncientMetagenomeDir

Anyone who adds metadata will be included on the next publication 🙂

GitHub
GitHub - SPAAM-community/AncientMetagenomeDir: Repository containing lists of all published ancient metagenome samples (and related)
Repository containing lists of all published ancient metagenome samples (and related) - GitHub - SPAAM-community/AncientMetagenomeDir: Repository containing lists of all published ancient metageno...
Original URL: https://github.com/SPAAM-community/AncientMetagenomeDir
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-12-13 09:18:11

*Thread Reply:* As you've got only 7 genomes it would probably take only about 30m for you

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-12-13 09:18:45

*Thread Reply:* (sorry to evangelise 😆 )

Joanna H. Bonczarowska (j.bonczarowska@ikmb.uni-kiel.de)
2022-12-13 09:19:55

*Thread Reply:* @James Fellows Yates only the pathogen-positive metagenomes? I will check it out :)

🙏 James Fellows Yates
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-12-13 09:19:58

*Thread Reply:* And also if you're on Twitter - have you made a twitter thread or something like that about he paper? We can retweet from the SPAAM account

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-12-13 09:20:10

*Thread Reply:* > only the pathogen-positive metagenomes? I will check it out 🙂 Not even, just the genomes themselves

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-12-13 09:20:46

*Thread Reply:* Unless you've analysed calculus or something (but I don't see that mentioned)

Joanna H. Bonczarowska (j.bonczarowska@ikmb.uni-kiel.de)
2022-12-13 09:21:33

*Thread Reply:* Unfortunately, I do not have twitter, not sure if any of my co-authors do.

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-12-13 09:21:45

*Thread Reply:* Ok, I can tweet juts the paper 🙂

Joanna H. Bonczarowska (j.bonczarowska@ikmb.uni-kiel.de)
2022-12-13 09:21:51

*Thread Reply:* Thank you

Joanna H. Bonczarowska (j.bonczarowska@ikmb.uni-kiel.de)
2022-12-13 09:21:55

*Thread Reply:* ! :)

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-12-13 09:25:48

*Thread Reply:* https://twitter.com/spaam_community/status/1602580490736787457

twitter
} SPAAM-community (https://twitter.com/spaam_community/status/1602580490736787457)
📃 New <b>#AncientMetagenomics</b> paper from Joanna Bonczarowska &amp; colleagues, with ancient genome recovery of hepatitis B virus, parvovirus B19, variola virus, and Mycobacterium leprae in <b>#Medieval</b> Europe! <https://doi.org/10.1186/s13059-022-02806-8> #ancientDNA <b>#palaeogenomics</b>
Original URL: https://twitter.com/spaam_community/status/1602580490736787457
Twitter
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2022-12-13 09:25:56

*Thread Reply:* I hopes thats Ok

Joanna H. Bonczarowska (j.bonczarowska@ikmb.uni-kiel.de)
2022-12-13 09:26:27

*Thread Reply:* That’s great thank you :)

irinavelsko (irinavelsko@gmail.com)
2023-01-08 18:09:17

Hi All, can anyone suggest papers that have looked at the causes of DNA degradation in ancient samples? Particularly any reviews?

Kelly Blevins (blevinske1@gmail.com)
2023-01-11 15:49:48

*Thread Reply:* https://royalsocietypublishing.org/doi/10.1098/rspb.2004.2813 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1802572/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC96698/ The first chapter of the book has a good table on damage types

PubMed Central (PMC)
Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis
Although ancient DNA (aDNA) miscoding lesions have been studied since the earliest days of the field, their nature remains a source of debate. A variety of conflicting hypotheses exist about which miscoding lesions constitute true aDNA damage as opposed ...
Original URL: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1802572/
PubMed Central (PMC)
DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA
We show that DNA molecules amplified by PCR from DNA extracted from animal bones and teeth that vary in age between 25 000 and over 50 000 years carry C→T and G→A substitutions. These substitutions can reach high proportions among the ...
Original URL: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC96698/
Ancient DNA Methods and Protocols second edition.pdf
irinavelsko (irinavelsko@gmail.com)
2023-01-12 08:01:02

*Thread Reply:* Thanks!

Pete Heintzman (peteheintzman@gmail.com)
2023-01-08 19:09:01

The ‘other’ Dabney et al. 2013 paper: https://cshperspectives.cshlp.org/content/5/7/a012567.full

cshperspectives.cshlp.org
Ancient DNA Damage
A new type of review journal, featuring comprehensive collections of expert review articles on important topics in the molecular life sciences
Original URL: https://cshperspectives.cshlp.org/content/5/7/a012567.full
irinavelsko (irinavelsko@gmail.com)
2023-01-09 08:35:26

*Thread Reply:* Thanks!

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-01-16 10:19:47

Interesting thread and papers about taxonomic classification/profiling: https://twitter.com/SilasKieser/status/1613868658811600896

twitter
} Dr. Silas Kieser @silask@mstdn.science (https://twitter.com/SilasKieser/status/1613868658811600896)
What a strong statement! Any other profiling method than metaphlan and mOTUs is wrong?! <https://twitter.com/fplazaonate/status/1613634493251784713>
Original URL: https://twitter.com/SilasKieser/status/1613868658811600896
Twitter
twitter
} Florian Plaza Oñate (https://twitter.com/fplazaonate/status/1613634493251784713)
<a href="https://twitter.com/DPortik">@DPortik</a> <a href="https://twitter.com/PacBio">@PacBio</a> <a href="https://twitter.com/nanopore">@nanopore</a> <a href="https://twitter.com/saltyscientist">@saltyscientist</a> <a href="https://twitter.com/ctitusbrown">@ctitusbrown</a> No matter the tool, trying to estimate species relative abundance by classifying reads is a bad idea if you don't know of which genomes your sample is made. Only those relying on marker genes are reliable.
Twitter
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-01-16 10:19:57

e.g.: https://www.nature.com/articles/s41592-021-01141-3

Nature
Challenges in benchmarking metagenomic profilers
Nature Methods - Many computational tools for metagenomic profiling have been developed, with different algorithms and features. This analysis shows that, when comparing these tools, the...
Original URL: https://www.nature.com/articles/s41592-021-01141-3
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-01-16 10:20:02

Or

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-01-16 10:20:03

https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-022-00207-7

BioMed Central
Investigating the impact of database choice on the accuracy of metagenomic read classification for the rumen microbiome - Animal Microbiome
Microbiome analysis is quickly moving towards high-throughput methods such as metagenomic sequencing. Accurate taxonomic classification of metagenomic data relies on reference sequence databases, and their associated taxonomy. However, for understudied environments such as the rumen microbiome many sequences will be derived from novel or uncultured microbes that are not present in reference databases. As a result, taxonomic classification of metagenomic data from understudied environments may be inaccurate. To assess the accuracy of taxonomic read classification, this study classified metagenomic data that had been simulated from cultured rumen microbial genomes from the Hungate collection. To assess the impact of reference databases on the accuracy of taxonomic classification, the data was classified with Kraken 2 using several reference databases. We found that the choice and composition of reference database significantly impacted on taxonomic classification results, and accuracy. In particular, NCBI RefSeq proved to be a poor choice of database. Our results indicate that inaccurate read classification is likely to be a significant problem, affecting all studies that use insufficient reference databases. We observed that adding cultured reference genomes from the rumen to the reference database greatly improved classification rate and accuracy. We also demonstrated that metagenome-assembled genomes (MAGs) have the potential to further enhance classification accuracy by representing uncultivated microbes, sequences of which would otherwise be unclassified or incorrectly classified. However, classification accuracy was strongly dependent on the taxonomic labels assigned to these MAGs. We therefore highlight the importance of accurate reference taxonomic information and suggest that, with formal taxonomic lineages, MAGs have the potential to improve classification rate and accuracy, particularly in environments such as the rumen that are understudied or contain many novel genomes.
Original URL: https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-022-00207-7
Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2023-01-16 10:20:35

this is my take on it https://github.com/genomewalker/bam-filter

GitHub
GitHub - genomewalker/bam-filter: A simple tool to calculate metrics from a BAM file and filter references with uneven coverages
A simple tool to calculate metrics from a BAM file and filter references with uneven coverages - GitHub - genomewalker/bam-filter: A simple tool to calculate metrics from a BAM file and filter refe...
Original URL: https://github.com/genomewalker/bam-filter
Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2023-01-16 10:24:26

here it provides abundance estimates and applies multiple filters beyond breadth

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2023-01-16 10:26:24

in any case having accurate abundance estimates of ancient metagenomic data is extremely difficult

👍 James Fellows Yates, Nikolay Oskolkov
Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2023-01-16 10:31:25

This is based on BAM files and is heavily coupled with our DBs and our metaDMG tool (https://www.biorxiv.org/content/10.1101/2022.12.06.519264v1)

bioRxiv
metaDMG – A Fast and Accurate Ancient DNA Damage Toolkit for Metagenomic Data
1. Motivation Under favourable conditions DNA molecules can persist for hundreds of thousands of years. Such genetic remains make up invaluable resources to study past assemblages, populations, and even the evolution of species. However, DNA is subject to degradation, and hence over time decrease to ultra low concentrations which makes it highly prone to contamination by modern sources. Strict precautions are therefore necessary to ensure that DNA from modern sources does not appear in the final data is authenticated as ancient. The most generally accepted and widely applied authenticity for ancient DNA studies is to test for elevated deaminated cytosine residues towards the termini of the molecules: DNA damage. To date, this has primarily been used for single organisms and recently for read assemblies, however, these methods are not applicable for estimating DNA damage for ancient metagenomes with tens and even hundreds of thousands of species. 2. Methods We present metaDMG, a novel framework and toolkit that allows for the estimation, quantification and visualization of postmortem damage for single reads, single genomes and even metagenomic environmental DNA by utilizing the taxonomic branching structure. It bypasses any need for initial classification, splitting reads by individual organisms, and realignment. We have implemented a Bayesian approach that combines a modified geometric damage profile with a beta-binomial model to fit the entire model to the individual misincorporations at all taxonomic levels. 3. Results We evaluated the performance using both simulated and published environmental DNA datasets and compared to existing methods when relevant. We find metaDMG to be an order of magnitude faster than previous methods and more accurate – even for complex metagenomes. Our simulations show that metaDMG can estimate DNA damage at taxonomic levels down to 100 reads, that the estimated uncertainties decrease with increased number of reads and that the estimates are more significant with increased number of C to T misincorporations. 4. Conclusion metaDMG is a state-of-the-art program for aDNA damage estimation and allows for the computation of nucleotide misincorporation, GC-content, and DNA fragmentation for both simple and complex ancient genomic datasets, making it a complete package for ancient DNA damage authentication. ### Competing Interest Statement The authors have declared no competing interest.
Original URL: https://www.biorxiv.org/content/10.1101/2022.12.06.519264v1
Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2023-01-16 10:32:41

filterBAM applies different filters beyond the traditional ones like positional entropy of the reads and report a few abundance estimates

👍 Nikolay Oskolkov
Nico Rascovan (nicorasco@gmail.com)
2023-01-16 10:46:01

I strongly recommend you to take a look at @Antonio Fernandez-Guerra take on all this (i.e., his pre-prints and github). He is applying it to the analyses of ancient microbial genomes from sediments, he recently explained us many of them in more detail in a visit to our lab, and I really loved it! @Antonio Fernandez-Guerra, you should give a seminar for the SPAAM community! Shouldn’t we have one monthly seminar/Lecture in SPAAM?

👍 Nikolay Oskolkov
👍:skin_tone_6: Miriam Bravo
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-01-16 10:46:28

*Thread Reply:* If you volunteer to set it up/run it @Nico Rascovan 😉

Nico Rascovan (nicorasco@gmail.com)
2023-01-16 10:47:29

*Thread Reply:* I’ll talk with the people of my team to organize it, all right! It’s just setting up one seminar per month, not big deal I hope ;)

👍 James Fellows Yates
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-01-16 10:48:11

*Thread Reply:* Note that @Maria Lopopolo is already running the #spaamtisch!

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-01-16 10:48:20

*Thread Reply:* Could also consider integrating the two

Nico Rascovan (nicorasco@gmail.com)
2023-01-16 10:48:24

*Thread Reply:* I am aware… yes

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-01-16 10:48:27

*Thread Reply:* Evening seminar style thing

Nico Rascovan (nicorasco@gmail.com)
2023-01-16 10:48:33

*Thread Reply:* sure, it’s a good idea

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-01-16 10:48:38

*Thread Reply:* (sponteaenous ly, )

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-01-16 10:48:45

*Thread Reply:* > I am aware… yes Needed a way to ping her 😉

Jasmin Frangenberg (jasmin.frangenberg@hki-jena.de)
2023-01-17 14:08:01

New mapping pipeline (in snakemake 👀) https://pubmed.ncbi.nlm.nih.gov/36637197

PubMed
Mapache: a flexible pipeline to map ancient DNA - PubMed
The list of software (and their references) used in the pipeline and the benchmark results can be found in the Supplementary files. An extensive manual is provided at <https://github.com/sneuensc/mapache/wiki>.
Original URL: https://pubmed.ncbi.nlm.nih.gov/36637197
Alex Hübner (alexander_huebner@eva.mpg.de)
2023-01-17 15:40:57

Congratulations to @Samuel Neuenschwander @Diana Ivette Cruz Dávalos @Davide Bozzi!

🙌 Jasmin Frangenberg, Nikolay Oskolkov
🙌:skin_tone_6: Miriam Bravo
🙌:skin_tone_5: Shreya
Miriam Bravo (bravolomiriam@gmail.com)
2023-01-17 22:23:59

Ancient pathogens provide a window into health and well-being https://www.pnas.org/doi/10.1073/pnas.2209476119

👍 James Fellows Yates, Davide Bozzi
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-01-20 08:27:26

Congrats to @Katherine Eaton!

https://www.nature.com/articles/s42003-022-04394-6

Nature
Plagued by a cryptic clock: insight and issues from the global phylogeny of Yersinia pestis
Communications Biology - The emergence of the plague pathogen throughout history is investigated using molecular clock modelling and phylogenetic analyses.
Original URL: https://www.nature.com/articles/s42003-022-04394-6
👍 Nikolay Oskolkov, Mohamed Sarhan, Hannah Moots, Gunnar Neumann
👀 Ian Light
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-01-23 07:00:21

*Thread Reply:* From the people who brought MixOmixs @irinavelsko

👍 irinavelsko
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-01-26 06:05:13

https://www.frontiersin.org/articles/10.3389/fevo.2022.888421/full

Frontiers
MetaDamage tool: Examining post-mortem damage in sedaDNA on a metagenomic scale
The use of metagenomic datasets to support ancient sedimentary DNA (sedaDNA) for paleoecological reconstruction has been demonstrated to be a powerful tool to understand multi-organism responses to climatic shifts and events. Authentication remains integral to the ancient DNA discipline, and this extends to sedaDNA analysis. Furthermore, distinguishing authentic sedaDNA from contamination or modern material also allows for a better understanding of broader questions in sedaDNA research, such as formation processes, source and catchment, and post-depositional processes. Existing tools for the detection of damage signals are designed for single-taxon input, require a priori organism specification, and require a significant number of input sequences to establish a signal. It is therefore often difficult to identify an established cytosine deamination rate consistent with ancient DNA across a sediment sample. In this study, we present MetaDamage, a tool that examines cytosine deamination on a metagenomic (all organisms) scale for multiple previously undetermined taxa and can produce a damage profile based on a few hundred reads. We outline the development and testing of the MetaDamage tool using both authentic sedaDNA sequences and simulated data to demonstrate the resolution in which MetaDamage can identify deamination levels consistent with the presence of ancient DNA. The MetaDamage tool offers a method for the initial assessment of the presence of sedaDNA and a better unde...
Original URL: https://www.frontiersin.org/articles/10.3389/fevo.2022.888421/full
👍 Nikolay Oskolkov, Davide Bozzi, Sterling Wright
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-01-26 06:06:07

From Rosie Everett and ex-SPAAM Becky Cribdon in Warwick

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-01-26 06:08:36

TL;DR Damage profiles from BLAST output

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-01-26 06:09:08

With some extra stats about confidence in the profile

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-01-28 07:10:01

@Camila Duitama @Nico Rascovan

You post a preprint on an ancient metagenomic source tracking tool and you don't post it here 😱😱😱?!?

Congrats though!

https://www.biorxiv.org/content/10.1101/2023.01.26.525439v1?rss=1

bioRxiv
decOM: Similarity-based microbial source tracking of ancient oral samples using k-mer-based methods
Background: The analysis of ancient oral metagenomes from archaeological human and animal samples is largely confounded by contaminant DNA sequences from modern and environmental sources. Existing methods for Microbial Source Tracking (MST) estimate the proportions of environmental sources, but do not perform well on ancient metagenomes. We developed a novel method called decOM for Microbial Source Tracking and classification of ancient and modern metagenomic samples using k-mer matrices. Results: We analysed a collection of 360 ancient oral, modern oral, sediment/soil and skin metagenomes, using stratified five-fold cross-validation. decOM estimates the contributions of these source environments in ancient oral metagenomic samples with high accuracy, outperforming two state-of-the-art methods for source tracking, FEAST and mSourceTracker. Conclusions: decOM is a high-accuracy microbial source tracking method, suitable for ancient oral metagenomic data sets. The decOM method is generic and could also be adapted for MST of other ancient and modern types of metagenomes. We anticipate that decOM will be a valuable tool for MST of ancient metagenomic studies. ### Competing Interest Statement The authors have declared no competing interest.
Original URL: https://www.biorxiv.org/content/10.1101/2023.01.26.525439v1?rss=1
👍 Nikolay Oskolkov, Jasmin Frangenberg, Louis L'Hôte
👍:skin_tone_3: Meriam van Os
❤️ Camila Duitama, Maria Lopopolo, Kelly Blevins
Camila Duitama (camiladuitama@gmail.com)
2023-01-30 22:17:14

Hi @James Fellows Yates and everyone! We had to post the preprint at the last minute, as we are preparing another submission 🙂. We are looking forward to hearing your comments, we hope decOM will help the aDNA community with your analysis 🧹🦷.

:mask_parrot: James Fellows Yates, Biancamaria Bonucci
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-01-31 07:08:04

https://www.biorxiv.org/content/10.1101/2023.01.24.524926v1

👍 Nikolay Oskolkov
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-01-31 09:58:35

Preprint of a review from @Abby Gancz as well!

https://f1000research.com/articles/12-109

f1000research.com
F1000Research Article: Studying ancient human oral microbiomes could yield insights into the evolutionary history of noncommunicable diseases.
Read the latest article version by Abigail S Gancz, Laura S Weyrich, at F1000Research.
Original URL: https://f1000research.com/articles/12-109
🎉 Pooja Swali, Gunnar Neumann, Miriam Bravo, Sterling Wright, Cameron Pauly, Kelly Blevins
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-02-07 06:59:33

Congrats to @Mohamed Sarhan @Christina Wurst!

https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-022-01509-7

BioMed Central
A nontuberculous mycobacterium could solve the mystery of the lady from the Franciscan church in Basel, Switzerland - BMC Biology
Background In 1975, the mummified body of a female has been found in the Franciscan church in Basel, Switzerland. Molecular and genealogic analyses unveiled her identity as Anna Catharina Bischoff (ACB), a member of the upper class of post-reformed Basel, who died at the age of 68 years, in 1787. The reason behind her death is still a mystery, especially that toxicological analyses revealed high levels of mercury, a common treatment against infections at that time, in different body organs. The computed tomography (CT) and histological analysis showed bone lesions in the femurs, the rib cage, and the skull, which refers to a potential syphilis case. Results Although we could not detect any molecular signs of the syphilis-causing pathogen Treponema pallidum subsp. pallidum, we realized high prevalence of a nontuberculous mycobacterium (NTM) species in brain tissue sample. The genome analysis of this NTM displayed richness of virulence genes and toxins, and similarity to other infectious NTM, known to infect immunocompromised patients. In addition, it displayed potential resistance to mercury compounds, which might indicate a selective advantage against the applied treatment. This suggests that ACB might have suffered from an atypical mycobacteriosis during her life, which could explain the mummy’s bone lesion and high mercury concentrations. Conclusions The study of this mummy exemplifies the importance of employing differential diagnostic approaches in paleopathological analysis, by combining classical anthropological, radiological, histological, and toxicological observations with molecular analysis. It represents a proof-of-concept for the discovery of not-yet-described ancient pathogens in well-preserved specimens, using de novo metagenomic assembly.
Original URL: https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-022-01509-7
🙏 Mohamed Sarhan
🙌 Nikolay Oskolkov, Sterling Wright
🙌:skin_tone_6: Miriam Bravo
🙌:skin_tone_2: Kelly Blevins
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-02-07 08:44:30

*Thread Reply:* @Mohamed Sarhan interested in adding your data to #ancientmetagenomedir?

👍 Mohamed Sarhan
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-02-07 08:44:33

*Thread Reply:* https://github.com/SPAAM-community/AncientMetagenomeDir/issues/1045

GitHub
Sarhan 2022 · Issue #1045 · SPAAM-community/AncientMetagenomeDir
Bug description <https://doi.org/10.1186/s12915-022-01509-7> Additional context <https://www.ebi.ac.uk/ena/browser/view/PRJEB44723>
Original URL: https://github.com/SPAAM-community/AncientMetagenomeDir/issues/1045
Mohamed Sarhan (mohamed.sarhan@eurac.edu)
2023-02-07 10:43:12

*Thread Reply:* Sure!

❤️ James Fellows Yates
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-02-07 07:00:30

And @Samuel Neuenschwander and @Diana Ivette Cruz Dávalos

https://academic.oup.com/bioinformatics/article/39/1/btad028/6986969?login=false

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-02-07 08:44:04

Also from @Mohamed Sarhan’s paper

:partyparrot: :partyparrot: :partyparrot: :partyparrot: :partyparrot:

image.png
🙌 Nikolay Oskolkov, Jasmin Frangenberg, Hannah Moots
🙌:skin_tone_6: Miriam Bravo
Mohamed Sarhan (mohamed.sarhan@eurac.edu)
2023-02-07 10:54:06

*Thread Reply:* Thanks again for your comments! They helped a lot with the peer-reviewing 😊 @James Fellows Yates @Nikolay Oskolkov @irinavelsko

👍 Nikolay Oskolkov, Zoé Pochon
❤️ James Fellows Yates
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-02-20 15:01:01

Not aDNA per-se, but could be very relevant given commonly fragmented assemblies, from @Raphael Eisenhofer!

https://www.nature.com/articles/s43705-023-00221-z

Nature
Impact of microbial genome completeness on metagenomic functional inference
ISME Communications - Impact of microbial genome completeness on metagenomic functional inference
Original URL: https://www.nature.com/articles/s43705-023-00221-z
👍 Sterling Wright
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-02-25 19:46:58

https://www.cell.com/current-biology/fulltext/S0960-9822(23)00133-1?returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0960982223001331%3Fshowall%3Dtrue|https://www.cell.com/current-biology/fulltext/S0960-9822(23)00133-1?returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0960982223001331%3Fshowall%3Dtrue

Current Biology
Emergence, continuity, and evolution of Yersinia pestis throughout medieval and early modern Denmark
Eaton et al. report 13 new ancient Yersinia pestis genomes from regions throughout medieval Denmark, demonstrating the continual evolution and reintroduction of Y. pestis strains throughout the second plague pandemic and highlighting how population-scale genomic evidence can be used to test hypotheses on disease mortality and epidemiology.
Original URL: https://www.cell.com/current-biology/fulltext/S0960-9822(23)00133-1?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0960982223001331%3Fshowall%3Dtrue
🎉 Gunnar Neumann
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-02-27 10:36:37

*Thread Reply:* incoming

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-02-27 10:36:43

*Thread Reply:*

mmc4.pdf
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-02-27 10:36:58

*Thread Reply:* (why, are you planning to help add it to #ancientmetagenomedir ? 😬 )

Ian Light (light@mpiib-berlin.mpg.de)
2023-02-27 10:39:03

*Thread Reply:* perhaps, but not for at least a few weeks -- the first author could as well 😉

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-02-27 10:39:22

*Thread Reply:* hahaha, teasing, no worries 😉

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-02-25 19:47:18

From @Katherine Eaton and co!

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-02-27 10:26:16

MetaPhlAn4: https://www.nature.com/articles/s41587-023-01688-w

Nature
Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4
Nature Biotechnology - Integration of metagenomic assemblies and microbial isolate genomes improves profiling of uncharacterized species.
Original URL: https://www.nature.com/articles/s41587-023-01688-w
👍 Camila Duitama, Florencia Alvarez Gallego, I-Ting Huang
Åshild (Ash) (ashild.v@gmail.com)
2023-03-06 09:41:40

https://www.nature.com/articles/s42003-023-04582-y

Nature
Rickettsia felis DNA recovered from a child who lived in southern Africa 2000 years ago
Communications Biology - Ancient genomic evidence for Rickettsia felis presence in human remains from 2000 years ago reframes previous hypotheses of R. felis as a novel or emergent pathogen in...
Original URL: https://www.nature.com/articles/s42003-023-04582-y
👍 James Fellows Yates, Biancamaria Bonucci, Alina Hiss
👍:skin_tone_2: Meriam Guellil
👍:skin_tone_6: Miriam Bravo
👀 Kelly Blevins
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-03-06 09:57:35

Really nice recommendations here on when to use Kraken2 vs MetaPhlAn3, and how to construct your database and/or which settings to use: https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000949

microbiologyresearch.org
From defaults to databases: parameter and database choice dramatically impact the performance of metagenomic taxonomic classification tools | Microbiology Society
In metagenomic analyses of microbiomes, one of the first steps is usually the taxonomic classification of reads by comparison to a database of previously taxonomically classified genomes. While different studies comparing metagenomic taxonomic classification methods have determined that different tools are ‘best’, there are two tools that have been used the most to-date: Kraken (k-mer-based classification against a user-constructed database) and MetaPhlAn (classification by alignment to clade-specific marker genes), the latest versions of which are Kraken2 and MetaPhlAn 3, respectively. We found large discrepancies in both the proportion of reads that were classified as well as the number of species that were identified when we used both Kraken2 and MetaPhlAn 3 to classify reads within metagenomes from human-associated or environmental datasets. We then investigated which of these tools would give classifications closest to the real composition of metagenomic samples using a range of simulated and mock samples and examined the combined impact of tool–parameter–database choice on the taxonomic classifications given. This revealed that there may not be a one-size-fits-all ‘best’ choice. While Kraken2 can achieve better overall performance, with higher precision, recall and F1 scores, as well as alpha- and beta-diversity measures closer to the known composition than MetaPhlAn 3, the computational resources required for this may be prohibitive for many researchers, and the default database and parameters should not be used. We therefore conclude that the best tool–parameter–database choice for a particular application depends on the scientific question of interest, which performance metric is most important for this question and the limit of available computational resources.
Original URL: https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000949
👍 Alex Hübner, Maria Lopopolo, Sterling Wright, Camila Duitama
👍:skin_tone_6: Miriam Bravo
👀 Kelly Blevins
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-03-13 15:08:41

Note a paper, but close enough (warning self PR):

https://twitter.com/jfy133/status/1635277477575811081

twitter
} James Fellows Yates | @jfy133@genomic.social (https://twitter.com/jfy133/status/1635277477575811081)
📯 A brand new <a href="https://twitter.com/nf_core">@nf_core</a> <a href="https://twitter.com/nextflowio">@nextflowio</a> pipeline for <b>#metagenomics</b> is out! 🧬 Looking to taxonomically classify or profile your short- or long- shotgun metagenomic reads, but don’t know which tool and/or database to use? 🤩 Why not use all with <https://nf-co.re/taxprofiler> ! [🧵1/8]
Original URL: https://twitter.com/jfy133/status/1635277477575811081
Twitter
👍 Nikolay Oskolkov, Pete Heintzman, Zoé Pochon
👍:skin_tone_6: Miriam Bravo
🎉 Pooja Swali, Zandra Fagernäs, Katerina Guschanski, Alina Hiss, Camila Duitama
💘 valentinav
🤩 Ivany Argueta, Bjorn Bartholdy
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-03-13 15:09:13

git (not aDNA specific but may add aDNA speicfic steps in the future)

🙌 Nico Rascovan, Mohamed Sarhan, Wenqin Yu, Jasmin Frangenberg
👏 Nico Rascovan, aidanva, Maria Lopopolo, Biancamaria Bonucci
👏:skin_tone_3: Katerina Guschanski
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-03-23 09:09:05

https://www.nature.com/articles/s41587-023-01696-w

Nature
Contamination source modeling with SCRuB improves cancer phenotype prediction from microbiome data
Nature Biotechnology - Modeling contamination sources over multiple samples enhances the analysis of microbiome data.
Original URL: https://www.nature.com/articles/s41587-023-01696-w
👍 Nikolay Oskolkov, aidanva, Biancamaria Bonucci, Sterling Wright, Camila Duitama
Joanna H. Bonczarowska (j.bonczarowska@ikmb.uni-kiel.de)
2023-03-27 17:14:22

“Ancient DNA and Forensic Microbiology” is now fully online and open for submissions!

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-03-27 17:31:00

*Thread Reply:* Do you have a link?

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-03-27 17:31:19

*Thread Reply:* Is this a journal or special issue of one?

Joanna H. Bonczarowska (j.bonczarowska@ikmb.uni-kiel.de)
2023-03-27 18:03:43

*Thread Reply:* It is a new section of Frontiers in Microbiology

Joanna H. Bonczarowska (j.bonczarowska@ikmb.uni-kiel.de)
2023-03-27 18:04:05

*Thread Reply:* https://www.frontiersin.org/journals/microbiology/sections/ancient-dna-and-forensic-microbiology

Frontiers
Frontiers in Microbiology | Ancient DNA and Forensic Microbiology
Advances biological research of microbes in ancient DNA and forensic investigations
Original URL: https://www.frontiersin.org/journals/microbiology/sections/ancient-dna-and-forensic-microbiology
👍 James Fellows Yates, Magdalena Haller-Caskie, Jasmin Frangenberg
Nico Rascovan (nicorasco@gmail.com)
2023-03-28 17:48:59

https://academic.oup.com/bib/article/24/2/bbad092/7077155

I wonder how this would perform on ancient DNA datasets… if it works well, it could be a good fast screening option..

👍 Nikolay Oskolkov
👍:skin_tone_6: Miriam Bravo
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-03-30 09:51:12

De Sanctis, B. (2022). Phylogenetic inference using ancient environmental DNA (Doctoral thesis). https://doi.org/10.17863/CAM.95210

https://aspace.repository.cam.ac.uk/handle/1810/347793

👍 Nikolay Oskolkov, Pete Heintzman
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-04-02 16:37:50

https://onlinelibrary.wiley.com/doi/10.1002/ajpa.24735

From Tanvi Honap, @Rita M Austin and co

👍 Nikolay Oskolkov, Sarah Johnson, Mohamed Sarhan, Nico Rascovan
🔥 Cameron Pauly, Miriam Bravo, Pooja Swali, Biancamaria Bonucci
🎉 Nihan D Dagtas
Nico Rascovan (nicorasco@gmail.com)
2023-04-03 11:39:45

*Thread Reply:* To be added in the AncientMetagenomeDir, right?

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-04-03 11:40:12

*Thread Reply:* No public data unfortunately:(

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-04-03 11:40:19

*Thread Reply:* As far as o can tell

Nico Rascovan (nicorasco@gmail.com)
2023-04-03 11:41:13

*Thread Reply:* PRJNA885571

Nico Rascovan (nicorasco@gmail.com)
2023-04-03 11:41:33

*Thread Reply:* but in sra, not yet in ENA

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-04-03 11:44:00

*Thread Reply:* Where did you find that?!

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-04-03 11:44:21

*Thread Reply:* I looked through the paper twice yday?!

irinavelsko (irinavelsko@gmail.com)
2023-04-03 11:49:15

*Thread Reply:* It's hidden if you're on the website, click the Open Research dropdown at the end of the page

👏 Nico Rascovan
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-04-03 12:14:39

*Thread Reply:* FML.

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-04-03 12:14:55

*Thread Reply:* Thanks @irinavelsko I guess that's a lesson in not looking via phone

irinavelsko (irinavelsko@gmail.com)
2023-04-03 12:27:59

*Thread Reply:* It's not at all obvious, it took me a while to find it

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-04-03 12:29:43

*Thread Reply:* It's terrible isn't it?!?

irinavelsko (irinavelsko@gmail.com)
2023-04-03 12:30:00

*Thread Reply:* It really is

Nico Rascovan (nicorasco@gmail.com)
2023-04-03 11:39:53

https://www.nature.com/articles/s42003-023-04723-3

Nature
Permafrost preservation reveals proteomic evidence for yak milk consumption in the 13th century
Communications Biology - Proteomic evidence from permafrost human dental calculus indicates consumption of yak milk in Mongolia as early as 1270 CE.
Original URL: https://www.nature.com/articles/s42003-023-04723-3
🎉 Christina Warinner
👍:skin_tone_6: Miriam Bravo
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-04-04 09:00:15

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10061425/

PubMed Central (PMC)
Contamination detection and microbiome exploration with GRIMER
Contamination detection is a important step that should be carefully considered in early stages when designing and performing microbiome studies to avoid biased outcomes. Detecting and removing true contaminants is challenging, especially in low-biomass ...
Original URL: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10061425/
👍 Camila Duitama
👍:skin_tone_3: Meriam van Os
Bjorn Bartholdy (bpbartholdy@pm.me)
2023-04-09 19:35:11

*Thread Reply:* Love the acronym 😆

:partyparrot: Wenqin Yu
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-04-16 12:39:45

https://doi.org/10.1111/1758-2229.13157

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-05-04 21:20:16

From @Alex Hübner, @Anan Ibrahim and co!

https://www.science.org/doi/10.1126/science.adf5300

🎉 Bjorn Bartholdy, Cameron Pauly, Nikolay Oskolkov, Pete Heintzman, Miriam Bravo, Mohamed Sarhan, Biancamaria Bonucci, Sterling Wright, irinavelsko, Jasmin Frangenberg, Alina Hiss, Maria Spyrou, Zandra Fagernäs, Christina Warinner, Luisa Sacristan, Piotr Rozwalak
🙌 Jasmin Frangenberg, Christina Warinner, Zoé Pochon
❤️ Nico Rascovan, Christina Warinner, Sarah Johnson
😍 Kuldeep More, Christina Warinner
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-05-04 21:20:45

*Thread Reply:* Although this brings a dilemma now @Alex Hübner, how shall we integrate the new libraries into AncientMetagenomeDir 🤔

Mohamed Sarhan (mohamed.sarhan@eurac.edu)
2023-05-04 22:56:15

*Thread Reply:* Congratulations guys 🎉🎉🎉

❤️ Christina Warinner, James Fellows Yates
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-05-09 14:18:45

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10150486/

PubMed Central (PMC)
SNV-FEAST: microbial source tracking with single nucleotide variants
Elucidating the sources of a microbiome can provide insight into the ecological dynamics responsible for the formation of these communities. Source tracking approaches to date leverage species abundance information; however, single nucleotide variants ...
Original URL: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10150486/
👀 Camila Duitama, Maria Lopopolo, Biancamaria Bonucci, Miriam Bravo, Marica Baldoni
🙌 Nico Rascovan, Arve Lee
Freya Steinhagen (stu227847@mail.uni-kiel.de)
2023-05-16 12:17:23

Hi y'all, is there someone here who might be able to provide access to this article? Warinner, Christina (2022): An Archaeology of Microbes. In Journal of Anthropological Research 78 (4), pp. 420–458. DOI: https://www.journals.uchicago.edu/doi/10.1086/721976 (Please delete if this post is out of place), thank you in advance 🙂

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-05-16 12:18:12

*Thread Reply:* @Tina Warinner?

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-05-16 12:18:20

*Thread Reply:* But this is the right place @Freya Steinhagen 🙂

👍 Freya Steinhagen
Yuti Gao (yuga3894@colorado.edu)
2023-05-16 13:18:58

*Thread Reply:* I happened to have just read this article!

Warinner_2022_An Archaeology of Microbes.pdf
🙏 Freya Steinhagen
❤️ James Fellows Yates, Gunnar Neumann
Freya Steinhagen (stu227847@mail.uni-kiel.de)
2023-05-16 13:20:06

*Thread Reply:* Wow, that was fast! Thanks a lot <3

🍻 Yuti Gao
Tina Warinner (twarinner@gmail.com)
2023-05-18 16:56:13

*Thread Reply:* Sorry - just seeing this now. Thanks for sending it @Yuti Gao!

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-05-26 20:08:07

From @Bjorn Bartholdy https://www.biorxiv.org/content/10.1101/2023.05.23.541904v1.full

👍 Nikolay Oskolkov, Bjorn Bartholdy, Cameron Pauly, Zandra Fagernäs
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-05-30 18:46:50

Congrats to @Pooja Swali et al!

https://www.nature.com/articles/s41467-023-38393-w

Nature
Yersinia pestis genomes reveal plague in Britain 4000 years ago
Nature Communications - An extinct prehistoric plague lineage of Yersinia pestis has been documented from Central Europe to Asia during the Late Neolithic and Bronze Age. Here, Swali et al. show...
Original URL: https://www.nature.com/articles/s41467-023-38393-w
👍 Nikolay Oskolkov
🎉 Miriam Bravo, Gunnar Neumann, Biancamaria Bonucci, Åshild (Ash), Meriam Guellil, Alina Hiss, Ian Light, Maria Lopopolo, Maria Zicos
❤️ Pooja Swali
Piotr Rozwalak (pioroz4@amu.edu.pl)
2023-06-02 09:45:54

Hello everyone, I'm excited to share my first paper on ancient metagenomics.

Our study shows that not only ancient bacteria but also their enemies, bacteriophages, can be reconstructed de novo from ancient metagenomes. Despite the perception of phages as highly variable due to mutations, recombinations, and gene transfers, we found that sometimes they can exhibit significant stability over time.

https://www.biorxiv.org/content/10.1101/2023.06.01.543182v1

:partyparrot: James Fellows Yates, Jasmin Frangenberg, Luisa Sacristan
🎉 Alex Hübner, Nikolay Oskolkov, Alina Hiss, Miriam Bravo, Jasmin Frangenberg, Mohamed Sarhan, Cameron Pauly, Luisa Sacristan
👍 Magdalena Haller-Caskie, Camila Duitama, Tina Warinner
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-06-02 09:48:18

*Thread Reply:* Nice figures btw!

Piotr Rozwalak (pioroz4@amu.edu.pl)
2023-06-02 09:50:36

*Thread Reply:* Thanks, prepared by #AndrzejZielezinski 😉

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-06-02 09:46:26

Congratulations!

👍 Piotr Rozwalak, Biancamaria Bonucci
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-06-11 09:46:40

https://www.biorxiv.org/content/10.1101/2023.06.10.544454v1.full.pdf+html|https://www.biorxiv.org/content/10.1101/2023.06.10.544454v1.full.pdf+html

(Congrats to @Antonio Fernandez-Guerra, finally ;) )

bioRxiv
A 2-million-year-old microbial and viral communities from the Kap København Formation in North Greenland
Using ancient environmental DNA (eDNA) we reconstructed microbial and viral communities from the Kap København Formation in North Greenland. We find pioneer microbial communities, along with likely dormant methanogens from the permafrost's seed bank. Our findings reveal that at the time of the formation, the terrestrial input of the Kap København site originated from a palustrine wetland, suggesting non-permafrost conditions. During this time, detection of methanogenic archaea and carbon processing pathways suggests a moderate strengthening of methane emissions through the northward expansion of wetlands. Intriguingly, we discover a remarkable sequence similarity (&gt;98%) between pioneer methanogens and present-day thawing permafrost counterparts. This suggests that not all microbes respond uniformly to environmental change over geological timescales, but that some microbial taxa's adaptability and resilience remain constant over time. Our findings further suggest that the composition of microbial communities is changing prior to plant communities as a result of global warming. ### Competing Interest Statement The authors have declared no competing interest.
Original URL: https://www.biorxiv.org/content/10.1101/2023.06.10.544454v1.full.pdf+html
👍 Nikolay Oskolkov, Pete Heintzman, Antonio Fernandez-Guerra, Luisa Sacristan, Biancamaria Bonucci, Piotr Rozwalak, Camila Duitama
🙌 Nico Rascovan
Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2023-06-12 06:54:25

*Thread Reply:* Thanks @James Fellows Yates Soon the second part with the 2Myr MAGs 😃

😆 James Fellows Yates
🙏 Nico Rascovan
Mohamed Sarhan (mohamed.sarhan@eurac.edu)
2023-06-12 22:55:42

https://wwwnc.cdc.gov/eid/article/29/6/23-0134_article

Emerging Infectious Diseases journal
Microscopic Evidence of Malaria Infection in Visceral Tissue from Medici Family, Italy
Microscopic Evidence of Malaria Infection in Visceral Tissue from Medici Family, Italy
Original URL: https://wwwnc.cdc.gov/eid/article/29/6/23-0134_article
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-06-13 07:53:24

https://www.nature.com/articles/s41559-023-02056-2

Nature
Inadvertent human genomic bycatch and intentional capture raise beneficial applications and ethical concerns with environmental DNA
Nature Ecology &amp; Evolution - The recovery of human genomic data from environmental DNA samples raises ethical questions regarding consent, privacy, surveillance and data ownership, which will...
Original URL: https://www.nature.com/articles/s41559-023-02056-2
👍 Nikolay Oskolkov, Jasmin Frangenberg
👀 Bjorn Bartholdy, Biancamaria Bonucci, Nihan D Dagtas
Maxime Borry (maxime.borry@gmail.com)
2023-06-14 18:51:22

https://www.biorxiv.org/content/10.1101/2023.06.13.544823v1

bioRxiv
VBCG: 20 validated bacterial core genes for phylogenomic analysis with high fidelity and resolution
Background Phylogenomic analysis has become an inseparable part of studies of bacterial diversity and evolution, and many different bacterial core genes have been collated and used for phylogenomic tree reconstruction. However, these genes have been selected based on their presence and single-copy ratio in all bacterial genomes, leaving out the gene's 'phylogenetic fidelity' unexamined. Results From 30,522 complete genomes covering 11,262 species, we examined 148 bacterial core genes that have been previously used for phylogenomic analysis. In addition to the gene presence and single-copy rations, we evaluated the gene's phylogenetic fidelity by comparing each gene's phylogeny with its corresponding 16S rRNA gene tree. Out of the 148 bacterial genes, 20 validated bacterial core genes (VBCG) were selected as the core gene set with the highest bacterial phylogenetic fidelity. Moreover, the smaller gene set resulted in a higher species presence in the tree than larger gene sets. Using Escherichia and Salmonella as examples of prominent bacterial foodborne pathogens, we demonstrated that the 20 VBCG produced phylogenies with higher fidelity and resolution at species and strain levels while 16S rRNA gene tree alone could not. Conclusion The 20 validated core gene set improves the fidelity and speed of phylogenomic analysis. Among other uses, this tool improves our ability to explore the evolution, typing and tracking of bacterial strains, such as human pathogens. We have developed a Python pipeline and a desktop graphic app (available on GitHub) for users to perform phylogenomic analysis with high fidelity and resolution. ### Competing Interest Statement The authors have declared no competing interest.
Original URL: https://www.biorxiv.org/content/10.1101/2023.06.13.544823v1
👍 Nikolay Oskolkov, Nico Rascovan
Jasmin Frangenberg (jasmin.frangenberg@hki-jena.de)
2023-07-14 11:36:04

Nice technology feature! https://www.nature.com/articles/d41586-023-02154-y Props to @Pooja Swali for advertising <#C02DCKJ54JX|no-stupid-questions> and #ancientmetagenomedir 😁

Nature
Germs, genes and soil: tales of pathogens past
Armed with DNA sequencers and powerful computational tools, archaeogeneticists are turning their attention towards ancient microbes to give bacteria their due in human history.
Original URL: https://www.nature.com/articles/d41586-023-02154-y
:partyparrot: James Fellows Yates, Luisa Sacristan, Pooja Swali, Biancamaria Bonucci, Bjorn Bartholdy
👍 Nikolay Oskolkov
👍:skin_tone_6: Miriam Bravo
🤩 Tina Warinner
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-07-19 19:15:16

https://www.biorxiv.org/content/10.1101/2023.07.17.549303v1?rss=1

bioRxiv
Benchmarking software tools for trimming adapters and merging next-generation sequencing data for ancient DNA
Ancient DNA is highly degraded, resulting in very short sequences. Reads generated with modern high-throughput sequencing machines are generally longer than ancient DNA molecules, therefore the reads often contain some portion of the sequencing adaptors. It is crucial to remove those adaptors, as they can interfere with downstream analysis. Furthermore, overlapping portions when DNA has been read forward and backward (paired-end) can be merged to correct sequencing errors and improve read quality. Several tools have been developed for adapter trimming and read merging, however, no one has attempted to evaluate their accuracy and evaluate their potential impact on downstream analyses. Through the simulation of sequencing data, seven commonly used tools were analyzed in their ability to reconstruct ancient DNA sequences through read merging. The analyzed tools exhibit notable differences in their abilities to correct sequence errors and identify the correct read overlap, but the most substantial difference is observed in their ability to calculate quality scores for merged bases. Selecting the most appropriate tool for a given project depends on several factors, although some tools such as fastp have some shortcomings, whereas others like leeHom outperform the other tools in most aspects. While the choice of tool did not result in a measurable difference when analyzing population genetics using principal component analysis, it is important to note that downstream analyses that rely on quality scores can be significantly impacted by the choice of tool. ### Competing Interest Statement The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. GR is the programmer behind leeHom. However, AL and LPL did not treat this program any differently from the others.
Original URL: https://www.biorxiv.org/content/10.1101/2023.07.17.549303v1?rss=1
🎉 Louis Kraft, Pete Heintzman, Camila Duitama, Kelly Blevins
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-07-19 19:15:44

Including @Louis Kraft!

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-08-02 06:49:39

https://www.biorxiv.org/content/10.1101/2023.07.28.550993v1

bioRxiv
Major data analysis errors invalidate cancer microbiome findings
We re-analyzed the data from a recent large-scale study that reported strong correlations between microbial organisms and 33 different cancer types, and that created machine learning predictors with near-perfect accuracy at distinguishing among cancers. We found at least two fundamental flaws in the reported data and in the methods: (1) errors in the genome database and the associated computational methods led to millions of false positive findings of bacterial reads across all samples, largely because most of the sequences identified as bacteria were instead human; and (2) errors in transformation of the raw data created an artificial signature, even for microbes with no reads detected, tagging each tumor type with a distinct signal that the machine learning programs then used to create an apparently accurate classifier. Each of these problems invalidates the results, leading to the conclusion that the microbiome-based classifiers for identifying cancer presented in the study are entirely wrong. These flaws have subsequently affected more than a dozen additional published studies that used the same data and whose results are likely invalid as well. ### Competing Interest Statement The authors have declared no competing interest.
Original URL: https://www.biorxiv.org/content/10.1101/2023.07.28.550993v1
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-08-02 06:50:00

Some interesting technical insights there on what can happen when you don't remove human DNA

👀 Bjorn Bartholdy, Camila Duitama
Ian Light (light@mpiib-berlin.mpg.de)
2023-08-02 16:03:51

THE DAY IS HERE !!!! https://f1000research.com/articles/12-926/v1 🔥:partyparrot::spaam:

f1000research.com
F1000Research Article: Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT.
Read the latest article version by Maxime Borry, Adrian Forsythe, Aida Andrades Valtueña, Alexander Hübner, Anan Ibrahim, Andrea Quagliariello, Anna E. White, Arthur Kocher, Åshild J. Vågene‬, Bjørn Peare Bartholdy, Diāna Spurīte, Gabriel Yaxal Ponce-Soto, Gunnar Neumann, I-Ting Huang, Ian Light, Irina M. Velsko, Iseult Jackson, Jasmin Frangenberg, Javier G. Serrano, Julien Fumey, Kadir T. Özdoğan, Kelly E. Blevins, Kevin G. Daly, Maria Lopopolo, Markella Moraitou, Megan Michel, Meriam van Os, Miriam J. Bravo-Lopez, Mohamed S. Sarhan, Nihan D. Dagtas, Nikolay Oskolkov, Olivia S. Smith, Ophélie Lebrasseur, Piotr Rozwalak, Raphael Eisenhofer, Sally Wasef, Shreya L. Ramachandran, Valentina Vanghi, Christina Warinner, James A. Fellows Yates, at F1000Research.
Original URL: https://f1000research.com/articles/12-926/v1
:catjam: Miriam Bravo, Nikolay Oskolkov, Mohamed Sarhan, Jasmin Frangenberg, Maxime Borry
👏:skin_tone_2: Meriam Guellil
:spaam: James Fellows Yates, Iseult, Nikolay Oskolkov, Mohamed Sarhan, Maxime Borry
👏 Carly Scott, Nikolay Oskolkov, Mohamed Sarhan, Maxime Borry
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-08-02 16:06:52

*Thread Reply:* it's alive

Marcel Keller (marcel.keller@ut.ee)
2023-08-02 17:33:23

this is not really SPAAM material, but I’m wondering what people here think about this paper: https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1010798 The only evidence for the age of the nematode is radiocarbon dating of the plant material of a rodent burrow where the nematodes were found. To me this is not sufficient evidence for these extraordinary claims.

journals.plos.org
A novel nematode species from the Siberian permafrost shares adaptive mechanisms for cryptobiotic survival with C. elegans dauer larva
Author summary Survival in extreme environments for prolonged periods is a challenge that only a few organisms, are capable of. It is not well understood, which molecular and biochemical pathways are utilized by such cryptobiotic organisms, and how long they might suspend life. Here, we show that a soil nematode Panagrolaimus kolymaensis, suspended life for 46,000 years in the Siberian permafrost. Through comparative analysis, we find that P. kolymaensis and model organism C. elegans utilize similar adaptive mechanisms to survive harsh environmental conditions for prolonged periods. Our findings here are important for the understanding of evolutionary processes because generation times could be stretched from days to millennia, and long-term survival of individuals of species can lead to the refoundation of otherwise extinct lineages.
Original URL: https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1010798
Christina Warinner (warinner@shh.mpg.de)
2023-08-03 15:07:24

*Thread Reply:* Agreed, I feel there is a lot lacking here

Maxime Borry (maxime.borry@gmail.com)
2023-08-04 16:45:16

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-023-05252-w#:~:text=The%20Microbiome%20Batch%20Effect%20Correction,the%20success%20of%20each%20method|https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-023-05252-w#:~:text=The%20Microbiome%20Batch%20Effect%20Correction,the%20success%20of%20each%20method.

BioMed Central
MBECS: Microbiome Batch Effects Correction Suite - BMC Bioinformatics
Despite the availability of batch effect correcting algorithms (BECA), no comprehensive tool that combines batch correction and evaluation of the results exists for microbiome datasets. This work outlines the Microbiome Batch Effects Correction Suite development that integrates several BECAs and evaluation metrics into a software package for the statistical computation framework R.
Original URL: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-023-05252-w#:~:text=The%20Microbiome%20Batch%20Effect%20Correction,the%20success%20of%20each%20method
👍 Nikolay Oskolkov, Biancamaria Bonucci
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-08-29 09:48:00

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10457426/

PubMed Central (PMC)
Refining biome labeling for large-scale microbial community samples: Leveraging neural networks and transfer learning
Microbiome research has generated an extensive amount of data, resulting in a wealth of publicly accessible samples. Accurate annotation of these samples is crucial for effectively utilizing microbiome data across scientific disciplines. However, a notable ...
Original URL: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10457426/
👍 Nikolay Oskolkov
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-08-29 09:48:11

Apparnetly they beieve they will also be able to identify the original source of 'ancient' MAGs?

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-08-29 19:37:40

Bacterial pangenome annotation: http://m.genome.cshlp.org/content/early/2023/08/24/gr.277733.123

👍 Davide Bozzi, I-Ting Huang
Camila Duitama (camiladuitama@gmail.com)
2023-09-04 18:48:22

https://www.nature.com/articles/s41598-023-36368-x#Sec4

Nature
Amelogenin peptide analyses reveal female leadership in Copper Age Iberia (c. 2900–2650 BC)
Scientific Reports - Amelogenin peptide analyses reveal female leadership in Copper Age Iberia (c. 2900–2650 BC)
Original URL: https://www.nature.com/articles/s41598-023-36368-x#Sec4
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-09-07 09:06:09

https://www.nature.com/articles/s41467-023-41174-0

Nature
Ancient Clostridium DNA and variants of tetanus neurotoxins associated with human archaeological remains
Nature Communications - The analysis of microbial genomes from human archaeological samples offers a snapshot of ancient pathogens. Here, Hodgins et al. analyze metagenomic datasets from 38 human...
Original URL: https://www.nature.com/articles/s41467-023-41174-0
🤔 Nikolay Oskolkov
👏 Mohamed Sarhan, Barbara
Nikolay Oskolkov (nikolay.oskolkov@scilifelab.se)
2023-09-07 09:09:15

*Thread Reply:* Damaged Clostridium tetani is super common to find in ancient human (and non-human) remains, but is it really an ancient pathogen, i.e. have something to do with ancient tetanus disease? Need to read the paper first 🙂

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-09-07 09:16:04

*Thread Reply:* No it's not an ancient pathologeb

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-09-07 09:16:10

*Thread Reply:* Abs they don't make their claim

👍 Nikolay Oskolkov
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-09-07 09:16:39

*Thread Reply:* Clostridium is general necrobiome, so it's not tetani Most likely

💯 Nikolay Oskolkov
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-09-07 09:17:03

*Thread Reply:* Aida did a masters thesis on it

Nikolay Oskolkov (nikolay.oskolkov@scilifelab.se)
2023-09-07 09:17:36

*Thread Reply:* I just read the abstract and it says "Thus, our ancient DNA analysis identifies DNA from neurotoxigenic C. tetani in archaeological human samples, and a novel variant of TeNT that can cause disease in mammals."

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-09-07 09:17:46

*Thread Reply:* The tree is fucking awful so m'identifico is a mess, as well as tetani being massively over represented

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-09-07 09:18:07

*Thread Reply:* Yes so they get the toxin that is normally right in tetani, and they tested it(which is the cool thing)

👍 Nikolay Oskolkov
Kevin Daly (dalyk1@tcd.ie)
2023-09-07 11:35:39

*Thread Reply:* @James Fellows Yates why do you call the tree awful? Choice of genomes to include, lack of support values, ... ?

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-09-07 11:55:24

*Thread Reply:* Sorry, meant the general taxonomy not the tree (and I'm not referring to the tree in the paper!)

The clostridium taxonomy and the naming system is purely based on physical characteristics and random tests but has no correspondence with the actusl genomes

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-09-07 11:55:36

*Thread Reply:* @aidanva can explain more

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-09-07 12:18:35

*Thread Reply:* Sorry to be clear!

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-09-07 12:18:40

*Thread Reply:* The is not necessarily bad!!!

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-09-07 12:18:53

*Thread Reply:* I've not read it closely

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-09-07 12:19:29

*Thread Reply:* But just remember the genus clostridium is a major part of the necrobiome, so it could still be ancient just most likely colonised immediately after death rather than being 'endogenous' to the invidual

💯 Nikolay Oskolkov
😲 Camila Duitama
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-09-07 12:19:54

*Thread Reply:* Just read the paper first, I believe the authors have been careful in waht they say their results are

Kevin Daly (dalyk1@tcd.ie)
2023-09-07 18:58:09

*Thread Reply:* No my 🤦‍♂️

Kevin Daly (dalyk1@tcd.ie)
2023-09-07 19:01:35

*Thread Reply:* Didn't intend to misrepresent what you wrote out-loud. Just wanted to understand!

The premortem/postmortem point is well made and one we think about. A cursed taxonomy, I didn't consider!

👍 James Fellows Yates
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-09-25 20:51:39

Congrats to @Nicola Vogel!!

https://besjournals.onlinelibrary.wiley.com/doi/10.1111/2041-210X.14214

🙌 Dawn lewis, Aleksandra Laura Pach, Jasmin Frangenberg, Camila Duitama, Yi Wang, Zoé Pochon, Liam Lanigan, Nikolay Oskolkov, Louis Kraft, Nicola Vogel
Camila Duitama (camiladuitama@gmail.com)
2023-10-09 10:22:55

*Thread Reply:* Gracias!

❤️ James Fellows Yates
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-10-04 07:39:03

Lots of food for thought here (ping @Aleksandra Laura Pach @Camila Duitama @irinavelsko @Nikolay Oskolkov)

https://www.mdpi.com/2076-2607/11/10/2478

One interesting quote:

> Another profiler KrakenUniq, an extension of Kraken, works on exact k-mer matching based on the HyperLogLog algorithm. KrakenUniq performed comparably to Kraken2 at the genus level but not so at the species level, establishing Kraken2 as a better profiler for ancient metagenome profiling. Furthermore, the database requirements for Kraken2 are less than those of KrakenUniq

MDPI
Benchmarking Metagenomic Classifiers on Simulated Ancient and Modern Metagenomic Data
Taxonomic profiling of ancient metagenomic samples is challenging due to the accumulation of specific damage patterns on DNA over time. Although a number of methods for metagenome profiling have been developed, most of them have been assessed on modern metagenomes or simulated metagenomes mimicking modern metagenomes. Further, a comparative assessment of metagenome profilers on simulated metagenomes representing a spectrum of degradation depth, from the extremity of ancient (most degraded) to current or modern (not degraded) metagenomes, has not yet been performed. To understand the strengths and weaknesses of different metagenome profilers, we performed their comprehensive evaluation on simulated metagenomes representing human dental calculus microbiome, with the level of DNA damage successively raised to mimic modern to ancient metagenomes. All classes of profilers, namely, DNA-to-DNA, DNA-to-protein, and DNA-to-marker comparison-based profilers were evaluated on metagenomes with varying levels of damage simulating deamination, fragmentation, and contamination. Our results revealed that, compared to deamination and fragmentation, human and environmental contamination of ancient DNA (with modern DNA) has the most pronounced effect on the performance of each profiler. Further, the DNA-to-DNA (e.g., Kraken2, Bracken) and DNA-to-marker (e.g., MetaPhlAn4) based profiling approaches showed complementary strengths, which can be leveraged to elevate the state-of-the-art of ancient metagenome profiling.
Original URL: https://www.mdpi.com/2076-2607/11/10/2478
👀 Aleksandra Laura Pach, Pete Heintzman, Camila Duitama
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-10-04 07:41:09

(Although a bit confused by this statement

> MetaPhlAn4 uses nucleotide BLAST (blastn) with a default E-value threshold of 1 × 10−6 to align reads to marker genes. > I'm pretty sure MP** uses bowtie2?

🤯 Mohamed Sarhan
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-10-04 07:42:38

(but I've not read the paper in depth)

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-10-04 07:42:56

Ah and the first author is here - congrats @Vaidehi Pusadkar!!!

Mohamed Sarhan (mohamed.sarhan@eurac.edu)
2023-10-04 08:41:48

Maybe they mixed version 1 and version 4

☝️ James Fellows Yates, Aleksandra Laura Pach
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-10-04 08:54:48

AHH yeah good point

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-10-04 08:55:04

Minor anyway

Nikolay Oskolkov (nikolay.oskolkov@scilifelab.se)
2023-10-04 09:03:51

Hmmm, looking at figures 1-4 I have difficulty seeing any differences in performance, @James Fellows Yates am I misunderstanding them?

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-10-04 09:07:32

*Thread Reply:* It's rather small yes the differences.

As we discussed at spaam5 databases are the bigger influenc/problem

But I think the point about memory usage in KU vs K2 is the more important but

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-10-04 09:07:35

*Thread Reply:* Bit**

Nikolay Oskolkov (nikolay.oskolkov@scilifelab.se)
2023-10-04 10:12:08

*Thread Reply:* Also, in addition to the database factor, how you filter Kraken2 and KrakenUniq outputs matters a lot

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-10-04 10:14:25

*Thread Reply:* Yes definitely, I honestly think we need to move on from which classifier to which parameters

👍 Nikolay Oskolkov, Zoé Pochon, Camila Duitama
❤️ Camila Duitama
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-10-04 10:15:45

*Thread Reply:* If anyone wants a project idea ;)

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-10-04 10:16:00

*Thread Reply:* I know a pipeline that can help with that 😬

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2023-10-06 09:10:36

*Thread Reply:* As important the filtering is, the parameters to build the db will have a huge impact on it. For example in k2, If you track the kmers for the different taxonomic assignments in dbs built with different kmer/minimizer lengths and minimizer spaces you will have a surprise in how the same read is assigned across the parameter space. Specially since the default db settings in k2 are not suitable for many of our datasets where the modal read lengths are fairly close to the default k2 k-mer length

👍 Nikolay Oskolkov, James Fellows Yates, Camila Duitama
Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2023-10-06 09:15:46

*Thread Reply:* Maybe not the most popular opinion, but I don’t think current k-mer based methods are suitable for our type of data.

Nikolay Oskolkov (nikolay.oskolkov@scilifelab.se)
2023-10-06 09:17:38

*Thread Reply:* Ha-ha, other approaches (alignment and de-novo) have own difficulties 🙂

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2023-10-06 09:18:20

*Thread Reply:* We need k-mer methods developed for aDNA

👍 Nikolay Oskolkov
Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2023-10-06 09:19:15

*Thread Reply:* Not adopting methods not designed for our type of data

☝️ Benjamin Vernot
Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2023-10-06 09:20:24

*Thread Reply:* Also we have very interesting new data structures that are very interesting for this problem, for example https://genomebiology.biomedcentral.com/articles/10.1186/s13059-023-02971-4

BioMed Central
Hierarchical Interleaved Bloom Filter: enabling ultrafast, approximate sequence queries - Genome Biology
We present a novel data structure for searching sequences in large databases: the Hierarchical Interleaved Bloom Filter (HIBF). It is extremely fast and space efficient, yet so general that it could serve as the underlying engine for many applications. We show that the HIBF is superior in build time, index size, and search time while achieving a comparable or better accuracy compared to other state-of-the-art tools. The HIBF builds an index up to 211 times faster, using up to 14 times less space, and can answer approximate membership queries faster by a factor of up to 129.
Original URL: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-023-02971-4
Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2023-10-06 09:21:16

*Thread Reply:* That have very interesting properties

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2023-10-06 09:22:12

*Thread Reply:* We are working on some solutions as it is very needed

👍 Nikolay Oskolkov
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-10-06 09:33:51

*Thread Reply:* What aren't you working on @Antonio Fernandez-Guerra 😉?

Maybe we need an emoji reaction for you. Someone asks a question and you just have to react on the post with an emoji and a bot will auto-post 'We are working on that' 😉

😂 Nikolay Oskolkov, Antonio Fernandez-Guerra
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-10-06 09:34:50

*Thread Reply:* > Maybe not the most popular opinion, but I don’t think current k-mer based methods are suitable for our type of data. I don't think that's an unpopular opinion! That's why people keep trying to use alignment stuff like MALT... they fall back to kmer stuff because of computational resource requirements ;)

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2023-10-06 09:35:10

*Thread Reply:* In our case we need to find ways to deal with billions of reads

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2023-10-06 09:35:31

*Thread Reply:* and where we only end up using a small proportion

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-10-06 09:36:20

*Thread Reply:* If you're interested in bloom filters (or variants): have you tried ganon (https://github.com/pirovc/ganon)?

pirovc/ganon
ganon classifies DNA sequences against large sets of genomic sequences efficiently, with download and update of databases (refseq/genbank), taxonomic profiling (ncbi/gtdb), binning and hierarchical classification, customized reporting and more
Website
<https://pirovc.github.io/ganon/>
Stars
69
Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2023-10-06 09:36:33

*Thread Reply:* yes, not working for our purpose

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-10-06 09:36:41

*Thread Reply:* Does that perform better than k2?

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-10-06 09:36:49

*Thread Reply:* What is your purpose in this case?

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2023-10-06 09:39:06

*Thread Reply:* i.e no mismatches allowed

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2023-10-06 09:40:27

*Thread Reply:* in the means that mismatches will not reduce the kmer you can generate

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2023-10-06 09:41:39

*Thread Reply:* from ganon’s paper https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7355301/#E2

PubMed Central (PMC)
ganon: precise metagenomics classification against large and up-to-date sets of reference sequences
The exponential growth of assembled genome sequences greatly benefits metagenomics studies. However, currently available methods struggle to manage the increasing amount of sequences and their frequent updates. Indexing the current RefSeq can take days ...
Original URL: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7355301/#E2
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-10-06 09:42:22

*Thread Reply:* I see. Have you considered asking the developer? He's extremely responsive, and he might be willing to add options to make it more amenable

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2023-10-06 09:42:22

*Thread Reply:* also it doesn’t have a damage model included

👍 James Fellows Yates
Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2023-10-06 09:43:25

*Thread Reply:* ganon is very good

👍 James Fellows Yates
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-10-06 09:45:23

*Thread Reply:* Good to know if it performs better than e.g. k2 still! But again might be worht speaking to the developer, might be good to integrate into that rather than reinventing the wheel

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2023-10-06 09:46:02

*Thread Reply:* it is not reinventing the wheel, the project is within another project looking at new data structures

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-10-06 09:46:12

*Thread Reply:* fair enogh

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2023-10-06 09:46:18

*Thread Reply:* that can index larger datasets

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2023-10-06 09:46:26

*Thread Reply:* another problem we have

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2023-10-06 09:46:46

*Thread Reply:* also is not a classifier

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2023-10-06 09:46:51

*Thread Reply:* what we are after

👍 James Fellows Yates
Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2023-10-06 09:47:58

*Thread Reply:* > Good to know if it performs better than e.g. k2 still! But again might be worht speaking to the developer, might be good to integrate into that rather than reinventing the wheel Yes, I don’t know why is not more used

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-10-06 09:49:05

*Thread Reply:* Age and Advertising 😆 😬

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2023-10-06 09:49:25

*Thread Reply:* I guess, but it touches all the good spots

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-10-06 09:49:35

*Thread Reply:* 💯

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-10-06 09:49:47

*Thread Reply:* I've already added it to taxprofiler so I hope it'll tickles peoples interest

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-10-06 09:49:57

*Thread Reply:* I think ganon also did well in CAMI/LEMMI

Nikolay Oskolkov (nikolay.oskolkov@scilifelab.se)
2023-10-06 09:50:56

*Thread Reply:* Guys, does anyone see a difference in F1-score in Figure 2 between ganon and K2?

Nikolay Oskolkov (nikolay.oskolkov@scilifelab.se)
2023-10-06 09:51:35

*Thread Reply:* is the advantage of ganon in just speed, i.e. not accuracy?

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-10-06 09:51:40

*Thread Reply:* (I think we are talking outside of the paper now I think)

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-10-06 09:52:10

*Thread Reply:* ()Ganon isn't tested in the paper)

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-10-06 09:52:23

*Thread Reply:* (whcih is @Antonio Fernandez-Guerra’s point that it's sad people arne't trying it out)

👍 Nikolay Oskolkov
Nikolay Oskolkov (nikolay.oskolkov@scilifelab.se)
2023-10-06 09:52:34

*Thread Reply:* Sorry, I meant in the Ganon paper

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2023-10-06 09:53:25

*Thread Reply:* For my taste, beside technical details, this is what makes ganon great: • multiple taxonomy integration (NCBI and GTDB) with lowest common ancestor (LCA) • read reassignment EM algorithm for multi-matching reads • hierarchical use of multiple databases • taxonomic and sequence abundance reports with genome size correction

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2023-10-06 09:53:40

*Thread Reply:* (I just copied from ganon githubs)

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2023-10-06 10:01:25

*Thread Reply:* > is the advantage of ganon in just speed, i.e. not accuracy? @Nikolay Oskolkov i usually don’t trust so much the benchmarks in the papers as it is very dataset dependent, and most of the time all methods perform fairly bad in our datasets 😅

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-10-06 10:03:47

*Thread Reply:* That's why we need a proper aDNA classifer benchmarking that is outside the racken and MetaPhlan families 😆

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2023-10-06 10:04:30

*Thread Reply:* yep

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-10-06 10:06:27

*Thread Reply:* And then we steal whatever fancy model Antonio and co are developing and add it to a classifier 🤣

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-10-06 10:06:35

*Thread Reply:* That performs best

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2023-10-06 10:06:44

*Thread Reply:* and there are many other problems. Check B of this figure. We didn’t find any other viruses beyond caudoviricites using nucleotides based methods. And we had to switch to amino acids

Figure-6.jpg
Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2023-10-06 10:07:35

*Thread Reply:* this is a extreme case as they are deep time samples, but shows the complexity and that can not be reduced to a single approach

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2023-10-06 10:11:00

*Thread Reply:* and we use quite comprehensive DBs for our profilings. For this pre-print we used:

image.png
👍 Nikolay Oskolkov
Camila Duitama (camiladuitama@gmail.com)
2023-10-09 10:32:48

*Thread Reply:* Perhaps you guys at @Antonio Fernandez-Guerra’s lab have a reliable enough dataset that can be used for benchmarking purposes ? (Thinking of the <#C05SQA7RA81|classifier-committee> )

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2023-10-09 10:45:29

*Thread Reply:* @Camila Duitama we have our internal datasets that we know them very well and we use them as benchmark, but they are not public yet. What I do for each analysis is to create a synthetic dataset based on the empirical data using https://github.com/genomewalker/aMGSIM. For example, to identify the best parameters for bowtie2 in the Kap K preprint: ```Best search parameters estimation To determine the optimal parameters for different searches, we utilised a workflow (https://github.com/aMG-tk/aMGSIM-smk) that combined the aMAW and aMGSIM (https://github.com/aMG-tk/aMGSIM) tools to generate synthetic metagenomes. We used ten samples from the Kap Kobenhavn formation (Supplementary Table 6) to model the community composition (bacteria, archaea, and viruses), the fragment length distribution, and the damage patterns for each reference. Each synthetic metagenome contained a maximum of 1000 damaged references (determined using Bayesian damage estimates), 500 non-damaged references, and 10 million reads. We then annotated these synthetic metagenomes using the aMAW taxonomy module, exploring different bowtie2 parameters (-N, -k [100, 250, 500, 750, 1000]), read ANI filtering thresholds (92%, 93%, 94%, 95%, 96%), and breadth filtering. We evaluated the sensitivity and specificity of the taxonomic profiling, the abundance estimations, and the damage estimations using precision, recall, F1, and F05 for classification problems, and Spearman correlation and median absolute error for quantitative comparisons.

In addition, we utilised the aMGSIM tool to track damage at the codon level to benchmark the MMseqs2 translated searches.```

genomewalker/aMGSIM
aMGSIM is an extension of MGSIM to create simulated ancient metagenome reads in multiple microbial synthetic communities.
Stars
3
Language
Python
👍 Camila Duitama
Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2023-10-09 10:46:54

*Thread Reply:* We are still using deamSIM as NGSNGS (https://github.com/RAHenriksen/NGSNGS) still don’t have an “amplicon mode”

RAHenriksen/NGSNGS
NGSNGS: Next generation simulator for next generation sequencing data
Stars
36
Language
C++
Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2023-10-09 10:47:41

*Thread Reply:* but we will transition to NGSNGS as soon it is ready

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2023-10-09 10:53:35

*Thread Reply:* btw, I added in bioconda https://anaconda.org/bioconda/gargammel-slim in case you are just interested on the three main programs of gargammel

🤩 James Fellows Yates
Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2023-10-09 10:53:55

*Thread Reply:* This a stripped version of Gargammel that only builds the programs fragSim, deamSim and adptSim. For a full Gargammel installation look at the gargammel package

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-10-09 10:53:57

*Thread Reply:* That's awesome!

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-10-09 10:54:01

*Thread Reply:* Thanks @Antonio Fernandez-Guerra!

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2023-10-09 10:54:57

*Thread Reply:* this package is what aMGSIM uses

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-10-14 12:24:27

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0292077

An... Interesting one... Maybe good a #spaamtisch discussion...

journals.plos.org
Edible flora in pre-Columbian Caribbean coprolites: Expected and unexpected data
Coprolites, or mummified feces, are valuable sources of information on ancient cultures as they contain ancient DNA (aDNA). In this study, we analyzed ancient plant DNA isolated from coprolites belonging to two pre-Columbian cultures (Huecoid and Saladoid) from Vieques, Puerto Rico, using shotgun metagenomic sequencing to reconstruct diet and lifestyles. We also analyzed DNA sequences of putative phytopathogenic fungi, likely ingested during food consumption, to further support dietary habits. Our findings show that pre-Columbian Caribbean cultures had a diverse diet consisting of maize (Zea mays), sweet potato (Ipomoea batatas), chili peppers (Capsicum annuum), peanuts (Arachis spp.), papaya (Carica papaya), tomato (Solanum lycopersicum) and, very surprisingly cotton (Gossypium barbadense) and tobacco (Nicotiana sylvestris). Modelling of putative phytopathogenic fungi and plant interactions confirmed the potential consumption of these plants as well as edible fungi, particularly Ustilago spp., which suggest the consumption of maize and huitlacoche. These findings suggest that a variety of dietary, medicinal, and hallucinogenic plants likely played an important role in ancient human subsistence and societal customs. We compared our results with coprolites found in Mexico and the United States, as well as present-day faeces from Mexico, Peru, and the United States. The results suggest that the diet of pre-Columbian cultures resembled that of present-day hunter-gatherers, while agriculturalists exhibited a transitional state in dietary lifestyles between the pre-Columbian cultures and larger scale farmers and United States individuals. Our study highlights differences in dietary patterns related to human lifestyles and provides insight into the flora present in the pre-Columbian Caribbean area. Importantly, data from ancient fecal specimens demonstrate the importance of ancient DNA studies to better understand pre-Columbian populations.
Original URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0292077
🙃 Aleksandra Laura Pach
😬 Hannes
👀 Camila Duitama
Hannes (hschroeder@sund.ku.dk)
2023-10-15 09:03:18

*Thread Reply:* A #spaamtisch discussion on this would be great if people are up for it @Maria Lopopolo @Biancamaria Bonucci @Aleksandra Laura Pach

:spaamtisch: James Fellows Yates, Biancamaria Bonucci, Maria Lopopolo, Liam Lanigan, Aleksandra Laura Pach
Aleksandra Laura Pach (alp@science.ku.dk)
2023-10-15 09:06:16

*Thread Reply:* Absolutely up for it!

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-10-14 12:26:11

(also ping @Hannes)

Hannes (hschroeder@sund.ku.dk)
2023-10-14 15:07:50

*Thread Reply:* 🙄

😆 James Fellows Yates
irinavelsko (irinavelsko@gmail.com)
2023-10-17 11:31:41

https://www.nature.com/articles/s41564-023-01484-x

Nature
Challenges and opportunities in sharing microbiome data and analyses
Nature Microbiology - An outline of best practices, resources and suggested improvements to ensure that the complexities inherent to microbial big data do not hamper accessibility.
Original URL: https://www.nature.com/articles/s41564-023-01484-x
👍 James Fellows Yates, Aleksandra Laura Pach, Camila Duitama, Jasmin Frangenberg
irinavelsko (irinavelsko@gmail.com)
2023-10-20 11:22:17

Hi All! We have a new preprint out with @Zandra Fagernäs on dental calculus in Oceania! How does the microbiome profile compare to other regions of the world? How well do these microbes reflect migration of their human hosts? How much of the microbial communiy is as-yet unexplored? https://www.biorxiv.org/content/10.1101/2023.10.18.563027v1

bioRxiv
Exploring archaeogenetic studies of dental calculus to shed light on past human migrations in Oceania
The Pacific islands have experienced multiple waves of human migrations, providing a case study for exploring the potential of using the microbiome to study human migration. We performed a metagenomic study of archaeological dental calculus from 103 ancient individuals, originating from 12 Pacific islands and spanning a time range of ~3000 years. Oral microbiome DNA preservation in calculus is far higher than that of human DNA in archaeological bone from the Pacific, and comparable to that seen in calculus from temperate regions. Variation in the microbial community composition was minimally driven by time period and geography within the Pacific, while comparison with samples from Europe, Africa, and Asia reveal the microbial communities of Pacific calculus samples to be distinctive. Phylogenies of individual bacterial species in Pacific calculus reflect geography. Archaeological dental calculus shows potential to yield information about past human migrations, complementing studies of the human genome. ### Competing Interest Statement The authors have declared no competing interest.
Original URL: https://www.biorxiv.org/content/10.1101/2023.10.18.563027v1
:mask_parrot: James Fellows Yates, Zandra Fagernäs, Aleksandra Laura Pach, Alina Hiss, Maria Zicos, Camila Duitama, Jasmin Frangenberg, Biancamaria Bonucci, Maria Lopopolo, Bjorn Bartholdy, Gabriel Yaxal Ponce Soto, Piotr Rozwalak
😍 Tina Warinner, Andrea quagliariello
🎉 Gunnar Neumann
Maria Lopopolo (maria.lopopolo1989@gmail.com)
2023-10-23 09:00:06

Dear @channel , we propose you to fill out this form if you want to anonymously publicise a paper that you or your team are publishing or have published. The media team will look at this form once a week and post it in the community #papers channel and on twitter and mastodon if you allow it 🙂

https://forms.gle/W2vxP6cpj318RiMN6

Google Docs
Papers for the spaam community
You can fill out this form if you want to anonymously publicise a paper that you or your team are publishing or have published. The media team will look at this form once a week and post it in the community <b>#papers</b> channel and on twitter and mastodon if you allow it.
Original URL: https://forms.gle/W2vxP6cpj318RiMN6
❤️ Biancamaria Bonucci, Victoria Oberreiter, Aleksandra Laura Pach
🎉 Gunnar Neumann
Zoé Pochon (zoe.pochon@gmail.com)
2023-10-23 13:38:50

The aMeta paper is finally out 🥳! This is a collaboration between bioinformaticians from SciLifeLab and the Centre for Palaeogenetics, involving (to name a few) @Nikolay Oskolkov, @Nora Bergfeldt, @Emrah Kırdök, me and other collaborators that are not all on the SPAAM slack! Basically, aMeta is an ancient metagenomics pipeline that takes FASTQ files as input, goes through classification with KrakenUniq, then generates a dynamic database for MALT alignment and provides several plots for authentication (edit distance, breadth, evenness of coverage, ANI, and more). It also generates an authentication score from 0 to 10 for each organism which can help you spare a lot of time so you can concentrate on the true ancient hits. Databases are available for download and the pipeline is on GitHub so feel free to try it out! https://genomebiology.biomedcentral.com/articles/10.1186/s13059-023-03083-9

BioMed Central
aMeta: an accurate and memory-efficient ancient metagenomic profiling workflow - Genome Biology
Analysis of microbial data from archaeological samples is a growing field with great potential for understanding ancient environments, lifestyles, and diseases. However, high error rates have been a challenge in ancient metagenomics, and the availability of computational frameworks that meet the demands of the field is limited. Here, we propose aMeta, an accurate metagenomic profiling workflow for ancient DNA designed to minimize the amount of false discoveries and computer memory requirements. Using simulated data, we benchmark aMeta against a current state-of-the-art workflow and demonstrate its superiority in microbial detection and authentication, as well as substantially lower usage of computer memory.
Original URL: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-023-03083-9
🙌 Ernst Johnson, Magdalena Haller-Caskie, Nico Rascovan, Martina Farese, Carly Scott, Minna Maunula
🎉 James Fellows Yates, Pete Heintzman, Erkin Alacamli, Nikolay Oskolkov, Ernst Johnson, Sierra Blunt, Ian Light, Gabriel Yaxal Ponce Soto, Biancamaria Bonucci, Luisa Sacristan, Nora Bergfeldt, Jasmin Frangenberg, Gunnar Neumann, Kadir Toykan Özdoğan, Ciara Wanket, Pooja Swali, Aleksandra Laura Pach, Alina Hiss, Nasreen Broomand, Nico Rascovan, Martina Farese, Yuejiao Huang, Stephanie Dolenz, Louis L'Hôte, Maria Lopopolo, Maria Zicos, Wenqin Yu, Elsa Peters
👏 James Fellows Yates, Pete Heintzman, Sarah Johnson, Nico Rascovan, Nihan D Dagtas, Davide Bozzi, Nicola Vogel
:mask_parrot: Camila Duitama, Jasmin Frangenberg, Cameron Ferguson, Dawn lewis
:party_dino: Alina Hiss, Kelly Blevins, Maria Zicos
❤️ Andrea quagliariello, Ania TSL, Benjamin G
👏:skin_tone_2: Meriam Guellil
👍 Hannes
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-10-23 13:48:47

*Thread Reply:* Congrats all!

:meow_party: Zoé Pochon, Nikolay Oskolkov, Biancamaria Bonucci, Emrah Kırdök
Nico Rascovan (nicorasco@gmail.com)
2023-10-23 16:13:49

*Thread Reply:* Congratulations @Nikolay Oskolkov et al.!

🙏 Nikolay Oskolkov, Emrah Kırdök
Alex Hübner (alexander_huebner@eva.mpg.de)
2023-10-23 22:20:25

*Thread Reply:* Congratulations!

🙏 Nikolay Oskolkov, Zoé Pochon, Emrah Kırdök
🙌 Zoé Pochon, Biancamaria Bonucci
Andrea quagliariello (quagliariello.andrea@gmail.com)
2023-10-24 11:27:11

*Thread Reply:* Congratulation @Zoé Pochon and to all the authors

🙏 Nikolay Oskolkov, Zoé Pochon, Emrah Kırdök
😊 Zoé Pochon
Maxime Borry (maxime.borry@gmail.com)
2023-11-02 20:23:47

https://journals.plos.org/water/article?id=10.1371/journal.pwat.0000171

journals.plos.org
Microbial community function and bacterial pathogen composition in pit latrines in peri-urban Malawi
Despite the widespread global reliance on pit latrines as improved sanitation systems, the decomposition of waste within pit latrines is poorly understood. One area needing elucidation is the characterization and function of microbial communities within pit latrines. To address this gap, we characterized the microbial communities of 55 lined pit latrines at three sampling layers from two communities in peri-urban Malawi. The microbial communities of the fecal sludge samples were analyzed for beta diversity, pathogen presence, and functional profiling. Household surveys were conducted and used to compare microbial community patterns to household characteristics and pit latrine use patterns. Compared to activated sludge, anaerobic digestion in municipal wastewater systems, and human gut microbiomes, pit latrines were found to contain unique microbial communities. While the microbial community composition as a whole did not vary by sampling depth, pathogen composition varied by sampling depth, location, and household water source. The inferred microbial function also varied by depth (e.g., increase in methanogens and decrease in aerobes with depth). The richness of lined pit latrines determined from surface samples from eight latrines was found to be representative for a given area. Samples from middle and lower depths collected using a Gulper pump did not provide more information on richness, a result that informs future sampling designs. These findings are important for improving waste-based epidemiology (WBE) approaches to understand community health and waste degradation characterization of lined pit latrines.
Original URL: https://journals.plos.org/water/article?id=10.1371/journal.pwat.0000171
👍 Dawn lewis, Maria Lopopolo, Barbara
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-11-06 18:35:33

biorxiv_bioinfo@biologists.social - Revisiting the Briggs ancient DNA damage model: a fast regression method to estimate postmortem damage  https://www.biorxiv.org/content/10.1101/2023.11.06.565746v1?med=mas

bioRxiv
Revisiting the Briggs ancient DNA damage model: a fast regression method to estimate postmortem damage
Motivation: One essential initial step in the analysis of ancient DNA is to authenticate its ancientness to ensure reliable conclusions. That is, meticulously assessing whether next-generation sequencing reads exhibit ancient characteristics, with a particular focus on the postmortem damage (PMD) signal induced by cytosine deamination in the fragments termini. We present a novel statistical method implementation in a fast multithreaded program ngsBriggs that enables the rapid quantification of PMD by calculation of the Briggs ancient damage model parameters (Briggs parameters). Results: Using a fast multinomial regression approach, ngsBriggs accurately models the Briggs parameters, quantifying the PMD signal from single and double-stranded DNA regions. We revisit and extend the original Briggs model, with ngsBriggs modeling PMD signals for contemporary sequencing platforms. Furthermore, ngsBriggs asserts itself as a reliable and consistent tool, by accurately estimating the Briggs parameters across a variety of contamination levels. The classification accuracy of ngsBriggs significantly exceeds the current tool available when discerning ancient- from modern sequencing reads to decontaminate samples. Our novel method and implementation ngsBriggs outperforms existing tools regarding computational speed and accuracy, establishing its practicality and usability. Our tool, ngsBriggs offers a practical and accurate toolset for researchers seeking to authenticate ancient DNA and improve the quality of their data. Availability: <https://github.com/lz398/metadamage> briggs ### Competing Interest Statement The authors have declared no competing interest.
Original URL: https://www.biorxiv.org/content/10.1101/2023.11.06.565746v1?med=mas
👍 Nikolay Oskolkov, Camila Duitama, Liam Lanigan, Wenqin Yu
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-11-07 16:35:47

Congrats to @Camila Duitama and co's deCOM (featured both at a previous #spaamtisch and at this year's summerschool) has finally been published!

https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-023-01670-3

BioMed Central
decOM: similarity-based microbial source tracking of ancient oral samples using k-mer-based methods - Microbiome
Background The analysis of ancient oral metagenomes from archaeological human and animal samples is largely confounded by contaminant DNA sequences from modern and environmental sources. Existing methods for Microbial Source Tracking (MST) estimate the proportions of environmental sources, but do not perform well on ancient metagenomes. We developed a novel method called decOM for Microbial Source Tracking and classification of ancient and modern metagenomic samples using k-mer matrices. Results We analysed a collection of 360 ancient oral, modern oral, sediment/soil and skin metagenomes, using stratified five-fold cross-validation. decOM estimates the contributions of these source environments in ancient oral metagenomic samples with high accuracy, outperforming two state-of-the-art methods for source tracking, FEAST and mSourceTracker. Conclusions decOM is a high-accuracy microbial source tracking method, suitable for ancient oral metagenomic data sets. The decOM method is generic and could also be adapted for MST of other ancient and modern types of metagenomes. We anticipate that decOM will be a valuable tool for MST of ancient metagenomic studies. Video Abstract
Original URL: https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-023-01670-3
🎉 Nikolay Oskolkov, Camila Duitama, Biancamaria Bonucci, aidanva, Maria Lopopolo, Sterling Wright, Mohamed Sarhan, Shreya, Wenqin Yu, Jasmin Frangenberg, Dawn lewis
:spaamtisch: Maria Lopopolo, Jasmin Frangenberg, Sarah Johnson
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-11-10 07:30:13

Preprint from @Kadir Toykan Özdoğan

https://www.researchsquare.com/article/rs-3568244/v1

Research Square
Archaeology meets Environmental Genomics: implementing sedaDNA in the study of the human past
Sedimentary ancient DNA (sedaDNA) has become one of the standard applications in the field of paleogenomics in recent years. It has been used for paleoenvironmental reconstructions, detecting the presence of prehistoric species in the absence of macro remains and even investigating the evoluti...
Original URL: https://www.researchsquare.com/article/rs-3568244/v1
👏 Aleksandra Laura Pach, Maria Lopopolo, Biancamaria Bonucci, Sterling Wright, Hannah Moots, Elena Zavala, Brina Zagorc, Oya Inanli, Benjamin Vernot
😮 Miriam Bravo
👍 Wenqin Yu, Jasmin Frangenberg, Dawn lewis
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-11-28 12:01:30

Anyone with access to https://www.sciencedirect.com/science/article/abs/pii/S1472979223000902

sciencedirect.com
Hit or miss - A metagenomic evaluation of intra-bone variability of host pathogen load in tuberculosis-infected human remains
Many sampling protocols have been established to successfully retrieve human DNA from archaeological remains, however the systematic detection of anci…
Original URL: https://www.sciencedirect.com/science/article/abs/pii/S1472979223000902
Iseult (ijackson@tcd.ie)
2023-11-28 12:03:44

*Thread Reply:* here you go :)

1-s2.0-S1472979223000902-main.pdf
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-11-28 12:05:23

*Thread Reply:*

tenor_gif977610692825246337.gif
🙂 Iseult
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-11-28 12:01:31

?

Abby Gancz (agancz@gmail.com)
2023-11-28 16:32:12

*Thread Reply:*

Hit or Miss.pdf
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-11-28 17:42:25

*Thread Reply:* Thanks @Abby Gancz however that looks really broken, the text runs off the page as does half to the images. But @Iseult already shared it above :)

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-11-30 06:59:55

Congrats to @Abby Gancz @Sterling Wright

https://www.nature.com/articles/s41564-023-01527-3

Nature
Ancient dental calculus reveals oral microbiome shifts associated with lifestyle and disease in Great Britain
Nature Microbiology - DNA analysis of ancient dental calculus samples revealed distinct oral microbial communities, including the archaeon Methanobrevibacter, which was associated with hygiene,...
Original URL: https://www.nature.com/articles/s41564-023-01527-3
:mask_parrot: Piotr Rozwalak, Pooja Swali, Mohamed Sarhan, Cameron Pauly, Alina Hiss, Hannah Moots, Sterling Wright, irinavelsko, Wenqin Yu
🙌 Sarah Johnson, Hannah Moots, Nikolay Oskolkov, Jasmin Frangenberg
Iseult (ijackson@tcd.ie)
2023-11-30 10:28:49

*Thread Reply:* Could I ask for someone with access to link a pdf? Thanks! and congrats! 🙂

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-11-30 10:46:00

*Thread Reply:* @irinavelsko should have one

irinavelsko (irinavelsko@gmail.com)
2023-11-30 10:47:06

*Thread Reply:* @Iseult

s41564-023-01527-3.pdf
Iseult (ijackson@tcd.ie)
2023-11-30 10:47:23

*Thread Reply:* Thanks a million!

Piotr Rozwalak (pioroz4@amu.edu.pl)
2023-12-10 15:13:25

If you are interested in how human gut bacteriophages diversified in tandem with urbanization and their associations with diseases, look at this:

"Phylogeny and disease links of a widespread and ancient gut phage lineage" https://www.biorxiv.org/content/10.1101/2023.08.29.555303v2

bioRxiv
Phylogeny and disease links of a widespread and ancient gut phage lineage
Viruses are a core component of the human microbiome, impacting health and disease through interactions with gut bacteria[1][1] and the immune system[2][2]. Most viruses in the human microbiome are bacteriophages, which exclusively infect bacteria. Individual gut bacteriophages can affect bacterial bile acid deconjugation[3][3], and can alter their infection strategy based on dietary content[4][4]. Up to recently, most studies of the gut virome have focused on low taxonomic scales (e.g., viral operational taxonomic units), hampering population-level analyses. We previously identified the expansive and widespread Candidatus Heliusviridae bacteriophage family in a cohort with inhabitants of Amsterdam, the Netherlands. Here, we study their biodiversity and evolution in a wide variety of human populations. With a detailed phylogeny based on sequences from six viral genome databases, we now propose the Candidatus order Heliusvirales to accommodate these viruses. We identify Ca. Heliusvirales viruses in 80% of 5,441 individuals across 39 studies, and also in nine out of thirteen analyzed metagenomes from ancient humans that lived in Europe and North America between 1,000 and 5,000 years ago. We show that a large Ca. Heliusvirales lineage has diversified starting at the appearance of Homo sapiens some 200,000-300,000 years ago. Ancient peoples and modern hunter-gatherers further have distinct Ca. Heliusvirales populations that are characterized by lower richness than modern urbanized people. Within urbanized people, those suffering from type 1 and type 2 diabetes, as well as inflammatory bowel disease, have higher Ca. Heliusvirales richness than healthy controls. We thus conclude that these ancient core members of the human gut virome have thrived with increasingly westernized lifestyles of the human population. ### Competing Interest Statement M.N. owns stock in, consults for, and has intellectual property rights in Caelus Health. He consults for Kaleido. None of these are directly relevant to the current paper. The remaining authors declare no competing interests. [1]: #ref-1 [2]: #ref-2 [3]: #ref-3 [4]: <b>#ref-4</b>
Original URL: https://www.biorxiv.org/content/10.1101/2023.08.29.555303v2
👍 James Fellows Yates, Jasmin Frangenberg, Wenqin Yu, Nikolay Oskolkov
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-12-10 16:33:20

*Thread Reply:* Do they publish their final genomes?

Piotr Rozwalak (pioroz4@amu.edu.pl)
2024-01-02 09:15:56

*Thread Reply:* I think not yet, I will ask about it 😉

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-12-18 08:36:36

Ancient chicken viruses 👆 with @Ophélie Lebrasseur @Ophélie Lebrasseur and others

🙌 Aurore Galtier, Gunnar Neumann, Maria Lopopolo, Magdalena Haller-Caskie
🎉 Alex Hübner, Ian Light
Maxime Borry (maxime.borry@gmail.com)
2023-12-18 14:22:21

https://pubmed.ncbi.nlm.nih.gov/36744896/

PubMed
Deduplication Improves Cost-Efficiency and Yields of De Novo Assembly and Binning of Shotgun Metagenomes in Microbiome Research - PubMed
In the last decade, metagenomics has greatly revolutionized the study of microbial communities. However, the presence of artificial duplicate reads raised mainly from the preparation of metagenomic DNA sequencing libraries and their impacts on metagenomic assembly and binning have never been brought …
Original URL: https://pubmed.ncbi.nlm.nih.gov/36744896/
👍 Liam Fitzstevens
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-12-18 14:22:55

*Thread Reply:* Hey @Benjamin Vernot you can update your slides saying 'HA TOLD YOU SO!'

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-12-18 14:23:43

*Thread Reply:* (admittedly this is relevant to different analysis but still

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2023-12-18 14:27:32

*Thread Reply:* also you might want to create super-reads before removing identical duplicates (100% identity on 100% length) so you can recover those reads that during adapter clipping and quality trimming will have shorter sequence lengths, but they are coming from the same template

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2023-12-18 14:29:51

*Thread Reply:* few months ago I added to aMGSIM the ability to add duplicates based on the duplicate distribution of empirical samples https://github.com/genomewalker/aMGSIM?tab=readme-ov-file#add-duplicates which uses the models from https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.13800

Benjamin Vernot (benjamin_vernot@eva.mpg.de)
2023-12-18 14:49:05

*Thread Reply:* hah! I love it, thanks @James Fellows Yates

Joanna H. Bonczarowska (j.bonczarowska@ikmb.uni-kiel.de)
2023-12-21 11:18:35

https://www.researchsquare.com/article/rs-3745869/latest

Research Square
Neolithic humans and dogs - transient reservoirs for Yersinia pestis
Yersinia pestis (Y. pestis) has been infecting humans since the Late Neolithic (LN). Whether those early infections were isolated zoonoses or initiators of a prehistoric Eurasia-wide pandemic remains unclear. We report the results of a pathogen screening on 133 LN human rema...
Original URL: https://www.researchsquare.com/article/rs-3745869/latest
:mask_parrot: James Fellows Yates, Biancamaria Bonucci, Hannah Moots, Rémi Barbieri, Nicolas da Silva, Florencia Alvarez Gallego, Magdalena Haller-Caskie, Aleksandra Laura Pach
😮 Kelly Blevins, Hannah Moots
🎉 Freya Steinhagen
🦠 Alina Hiss
Camila Duitama (camiladuitama@gmail.com)
2024-01-22 12:58:00

Not so recent but useful for those of you interested in aDNA from South America https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10670959/

PubMed Central (PMC)
Unraveling the Genetic Threads of History: mtDNA HVS-I Analysis Reveals the Ancient Past of the Aburra Valley
This article presents a comprehensive genetic study focused on pre-Hispanic individuals who inhabited the Aburrá Valley in Antioquia, Colombia, between the tenth and seventeenth centuries AD. Employing a genetic approach, the study analyzed maternal ...
Original URL: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10670959/
:meow_party: Luisa Sacristan, Maria Lopopolo, Ania TSL, Nikolay Oskolkov
👍 Constanza de la Fuente
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2024-01-24 06:50:35

Congrats to @Piotr Rozwalak!

https://www.nature.com/articles/s41467-023-44370-0

Nature
Ultraconserved bacteriophage genome sequence identified in 1300-year-old human palaeofaeces
Nature Communications - Bacterial viruses (phages) are generally recognised as rapidly evolving biological entities. Here, Rozwalak et al. analyse DNA sequence datasets generated from ancient...
Original URL: https://www.nature.com/articles/s41467-023-44370-0
:poop_party: Jasmin Frangenberg
🎉 Inés Barrenechea Angeles
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2024-01-24 06:51:15

*Thread Reply:* Fancy adding the genome to the 'Dir? 😏

Piotr Rozwalak (pioroz4@amu.edu.pl)
2024-01-24 11:15:25

*Thread Reply:* Sure 😄 , now is available in Genbank here: https://www.ncbi.nlm.nih.gov/nuccore/BK063464

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2024-01-24 20:17:37

Congrats to @Kerttu Majander!

https://www.nature.com/articles/s41586-023-06965-x

Nature
Redefining the treponemal history through pre-Columbian genomes from Brazil
Nature - Reconstruction of four Treponema pallidum genomes associated with human remains from around 2,000 years ago suggests that T. pallidum existed in the Americas and diverged to its modern...
Original URL: https://www.nature.com/articles/s41586-023-06965-x
🎉 Zandra Fagernäs, Gunnar Neumann, Iseult, Jasmin Frangenberg, Zoé Pochon, Meriam Guellil, Nelli-Johanna, Toni de Dios Martínez, Louis L'Hôte
😮 Miriam Bravo, Maria Lopopolo
👍 Magdalena Haller-Caskie
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2024-01-28 09:41:01

Ancient japanese palaeofaeces including@Kae Koganebuchi !

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0295924

journals.plos.org
Metagenomic analyses of 7000 to 5500 years old coprolites excavated from the Torihama shell-mound site in the Japanese archipelago
Coprolites contain various kinds of ancient DNAs derived from gut micro-organisms, viruses, and foods, which can help to determine the gut environment of ancient peoples. Their genomic information should be helpful in elucidating the interaction between hosts and microbes for thousands of years, as well as characterizing the dietary behaviors of ancient people. We performed shotgun metagenomic sequencing on four coprolites excavated from the Torihama shell-mound site in the Japanese archipelago. The coprolites were found in the layers of the Early Jomon period, corresponding stratigraphically to 7000 to 5500 years ago. After shotgun sequencing, we found that a significant number of reads showed homology with known gut microbe, viruses, and food genomes typically found in the feces of modern humans. We detected reads derived from several types of phages and their host bacteria simultaneously, suggesting the coexistence of viruses and their hosts. The food genomes provide biological evidence for the dietary behavior of the Jomon people, consistent with previous archaeological findings. These results indicate that ancient genomic analysis of coprolites is useful for understanding the gut environment and lifestyle of ancient peoples.
Original URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0295924
🎉 Yoshiki Wakiyama, Wenqin Yu, Piotr Rozwalak, Mohamed Sarhan, Gunnar Neumann
:poop_party: Liam Lanigan, Biancamaria Bonucci, Jasmin Frangenberg, Aleksandra Laura Pach, Kae Koganebuchi
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2024-01-30 09:35:18

A preprint from @Nikolay Oskolkov!

https://www.biorxiv.org/content/10.1101/2024.01.24.576930v1

bioRxiv
Unravelling the ancient fungal DNA from the Iceman’s gut
Here, we explore the possible ancient fungal species in the gut of Ötzi, the Iceman, a naturally mummified human found in the Tyrolean Alps (border between Italy and Austria). While ancient DNA (aDNA) has been extensively used to study human, animal, and plant evolution, this research focuses on ancient microbial diversity, specifically fungi. Fungal DNA is often underestimated in metagenomic samples, however here we hypothesise the possibility of retrieving ancient fungal sequences from Ötzi’s gut. A robust bioinformatic pipeline has been developed to detect and authenticate fungal aDNA from stomach, small intestine, and large intestine samples. We revealed the presence of Pseudogymnoascus genus, with P. destructans and P. verrucosus as possible species, that were particularly abundant in the stomach and small intestine. We suggest that Ötzi may have consumed these fungi accidentally, likely in association with other elements of his diet, and they thrived in his gut after his death due to their adaptability to harsh and cold environments. This research provides insight into the coexistence of ancient humans with specific fungal species and proposes and validates a conservative bioinformatic approach for detecting fungal aDNA in historical metagenomic samples. Significance statement Despite their essential interactions with all kingdoms of life, limited molecular studies have focused on ancient fungi. Here, we developed a thorough bioinformatic pipeline that allowed us to detect the presence of ancient DNA likely belonging to Pseudogymnoascus destructans and P. verrucosus in the gut of Ötzi, a human naturally mummified over 3,000 years ago in the Tyrolean Alps. Both species can survive harsh environmental conditions, and P. destructans is known for its pathogenicity, suggesting that Ötzi may have accidentally ingested them and providing valuable insights into how ancient humans coexisted with specific fungal species. We propose a highly reliable methodology for detecting ancient fungal DNA in metagenomic studies of historical samples that can have broader applications to understand ancient ecosystems and their interactions. ### Competing Interest Statement The authors have declared no competing interest.
Original URL: https://www.biorxiv.org/content/10.1101/2024.01.24.576930v1
:mask_parrot: Piotr Rozwalak, Carly Scott
👍 Nikolay Oskolkov
:spaamtisch: Maria Lopopolo
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2024-01-30 09:35:24

More almost poop!

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2024-01-31 06:01:11

Now some calculus, featuring @Claudio Ottoni!

https://www.nature.com/articles/s41598-024-52422-8

Nature
First archaeological evidence for ginger consumption as a potential medicinal ingredient in a late medieval leprosarium at St Leonard, Peterborough, England
Scientific Reports - First archaeological evidence for ginger consumption&amp;nbsp;as a potential medicinal ingredient in a late medieval leprosarium at St Leonard, Peterborough, England
Original URL: https://www.nature.com/articles/s41598-024-52422-8
🎉 Hannah Moots, Nikolay Oskolkov, Meriam Guellil, irinavelsko, Alina Hiss, Biancamaria Bonucci, Jasmin Frangenberg, Sierra Blunt
Joanna H. Bonczarowska (j.bonczarowska@ikmb.uni-kiel.de)
2024-02-01 11:52:15

Hello everyone, I would like to share our preprint with you! Maybe interesting 🙂 https://www.researchsquare.com/article/rs-3879251/v1

Research Square
Ancient DNA study provides clues to leprosy susceptibility in medieval Europe
Background Leprosy is a chronic infectious disease caused by Mycobacterium leprae (M. leprae) that reached an epidemic scale in the Middle Ages. Nowadays, the disease is absent in Europe and host genetic influences have been considered as a contributing factor to lep...
Original URL: https://www.researchsquare.com/article/rs-3879251/v1
👍 Nikolay Oskolkov, Biancamaria Bonucci, Alex Hübner, Jasmin Frangenberg, Zoé Pochon, Nicolas da Silva
🙌 Magdalena Haller-Caskie, Bjorn Bartholdy
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2024-02-16 04:47:14

Nice visualisation tool for SNPs on a MSA: https://github.com/aineniamh/snipit?tab=readme-ov-file

👍 Alex Hübner, Pooja Swali, Mohamed Sarhan, Liam Fitzstevens, Wenqin Yu, Biancamaria Bonucci
👀 Yoshiki Wakiyama, Maria Lopopolo, Miriam Bravo, Jasmin Frangenberg
👍:skin_tone_2: Meriam Guellil
👍:skin_tone_3: Meriam van Os
Camila Duitama (camiladuitama@gmail.com)
2024-02-21 11:28:10

Cases of trisomy 21 and trisomy 18 among historic and prehistoric individuals discovered from ancient DNA🙀 https://www.nature.com/articles/s41467-024-45438-1

Nature
Cases of trisomy 21 and trisomy 18 among historic and prehistoric individuals discovered from ancient DNA
Nature Communications - Information on the occurrence of aneuploidies in prehistory human populations are rare. Here, from a large screen of ancient human genomes and osteological examination, the...
Original URL: https://www.nature.com/articles/s41467-024-45438-1
🧬 Liam Lanigan, Marina Buffoli
🤔 Nikolay Oskolkov
👏 Rémi Barbieri
Mikkel Winther Pedersen (mwpedersen@sund.ku.dk)
2024-02-22 09:16:40

Morning all! I seem not to be able to connect to the cloud entry server, do you have this issue? @James Fellows Yates I hope you and the whole family made it through ok!

Mikkel Winther Pedersen (mwpedersen@sund.ku.dk)
2024-02-22 09:16:58

It worked earlier this morning

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2024-02-22 13:20:18

I think this is the wrong chat @Mikkel Winther Pedersen, will in the correct one

😂 Mikkel Winther Pedersen
Mikkel Winther Pedersen (mwpedersen@sund.ku.dk)
2024-02-22 14:16:15

*Thread Reply:* you are right!

Sterling Wright (sterlingwright2016@utexas.edu)
2024-03-01 14:34:40

New calculus paper comparing a 16S capture technique designed for dental calculus @Raphael Eisenhofer

https://peerj.com/articles/16770/

PeerJ
Benchmarking a targeted 16S ribosomal RNA gene enrichment approach to reconstruct ancient microbial communities
The taxonomic characterization of ancient microbiomes is a key step in the rapidly growing field of paleomicrobiology. While PCR amplification of the 16S ribosomal RNA (rRNA) gene is a widely used technique in modern microbiota studies, this method has systematic biases when applied to ancient microbial DNA. Shotgun metagenomic sequencing has proven to be the most effective method in reconstructing taxonomic profiles of ancient dental calculus samples. Nevertheless, shotgun sequencing approaches come with inherent limitations that could be addressed through hybridization enrichment capture. When employed together, shotgun sequencing and hybridization capture have the potential to enhance the characterization of ancient microbial communities. Here, we develop, test, and apply a hybridization enrichment capture technique to selectively target 16S rRNA gene fragments from the libraries of ancient dental calculus samples generated with shotgun techniques. We simulated data sets generated from hybridization enrichment capture, indicating that taxonomic identification of fragmented and damaged 16S rRNA gene sequences was feasible. Applying this enrichment approach to 15 previously published ancient calculus samples, we observed a 334-fold increase of ancient 16S rRNA gene fragments in the enriched samples when compared to unenriched libraries. Our results suggest that 16S hybridization capture is less prone to the effects of background contamination than 16S rRNA amplification, yielding a higher percentage of on-target recovery. While our enrichment technique detected low abundant and rare taxa within a given sample, these assignments may not achieve the same level of specificity as those achieved by unenriched methods.
Original URL: https://peerj.com/articles/16770/
👍 James Fellows Yates, Nikolay Oskolkov
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2024-03-02 03:20:34

*Thread Reply:* That's a really nice study, it reads really well in terms of the order of experiments 👏👏.

@Biancamaria Bonucci @Maria Lopopolo imo this would be a nice one for a spaamtisch and a tweet, lots of Qs about amplicon/metabarcoding came up at the ACAD workshop and so this would be timely

❤️ Sterling Wright, Biancamaria Bonucci
Sterling Wright (sterlingwright2016@utexas.edu)
2024-03-02 04:40:35

*Thread Reply:* Thank you! And sure we can set something up. I’m hoping to defend here soon and so I’m not sure if I’ll have time until the summer but maybe Ralph would be up for this?

❤️ Biancamaria Bonucci
Biancamaria Bonucci (biancamaria.bonucci@ut.ee)
2024-03-02 06:51:40

*Thread Reply:* Nice!! We can send you an e-mail and you guys can decide ☺️

👍 James Fellows Yates
Maria Lopopolo (maria.lopopolo1989@gmail.com)
2024-03-05 09:58:28

*Thread Reply:* It would be great I agree, @Sterling Wright you could also fill this out and let us know your availability :) https://docs.google.com/forms/d/e/1FAIpQLSc0Lb3kKm2sRTutY9Nyk58SN9Lg82VfUMtVvrEmVGmwHZxw/viewform?usp=sf_link

Sterling Wright (sterlingwright2016@utexas.edu)
2024-03-06 03:17:29

*Thread Reply:* Filled it out!

:spaamtisch: Maria Lopopolo
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2024-03-14 14:56:31

Congrats to @Ophélie Lebrasseur @Ophélie Lebrasseur!

https://academic.oup.com/ve/article/10/1/vead087/7523751

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2024-03-14 14:56:52

Ancient horse viruses!

🎉 Pete Heintzman, irinavelsko, Gunnar Neumann, Yuejiao Huang, Biancamaria Bonucci, Zoé Pochon, Nikolay Oskolkov, Florencia Alvarez Gallego, Alina Hiss, Ian Light, Luisa Sacristan, Wenqin Yu, Elisa Davis, Barbara
👏 Audrey Lin, aidanva
😲 Miriam Bravo, Biancamaria Bonucci, Ian Light
🦠 Alina Hiss, Louis L'Hôte
👏:skin_tone_2: Meriam Guellil
Miriam Bravo (bravolomiriam@gmail.com)
2024-03-27 14:45:35

https://academic.oup.com/mbe/article/41/3/msae017/7617356 Ancient Genomes From Bronze Age Remains Reveal Deep Diversity and Recent Adaptive Episodes for Human Oral Pathobionts by @Iseult

🙌 Nikolay Oskolkov, Biancamaria Bonucci, Louis L'Hôte, Zoé Pochon
❤️ Iseult, Biancamaria Bonucci, Sarah Johnson, Maria Lopopolo
👏 James Fellows Yates, Jasmin Frangenberg
🦷 Shreya, Zoé Pochon, Maria Lopopolo
🦠 Shreya
🪥 Shreya, Zoé Pochon
👅 Shreya
Shreya (shreya23@uchicago.edu)
2024-03-27 16:49:40

*Thread Reply:* Yayyyy I’ve been waiting for this! Congrats Iseult!

❤️ Iseult
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2024-04-06 07:02:36

Congrats to @Bing Sun @aidanva and co!

https://www.nature.com/articles/s41467-024-47358-6

Nature
Origin and dispersal history of Hepatitis B virus in Eastern Eurasia
Nature Communications - Hepatitis B virus is an ancient human pathogen that dates back more than 10,000 years. Here, the authors investigate the evolutionary history of the virus in Eastern Eurasia...
Original URL: https://www.nature.com/articles/s41467-024-47358-6
👍 Pete Heintzman, Sterling Wright, Zoé Pochon, Nikolay Oskolkov, Wenqin Yu, Åshild (Ash)
👏 Iseult, Jasmin Frangenberg, Alex Hübner, Megan Michel, Magdalena Haller-Caskie
❤️ Maria Lopopolo, Florencia Alvarez Gallego
:party_dino: Alina Hiss
👏:skin_tone_2: Meriam Guellil
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2024-04-16 07:12:28

@Nicola Vogel is on a roll!

https://www.biorxiv.org/content/10.1101/2024.04.12.589157v1?med=mas

bioRxiv
soibean: High-resolution Taxonomic Identification of Ancient Environmental DNA Using Mitochondrial Pangenome Graphs
Ancient environmental DNA (aeDNA) is becoming a powerful tool to gain insights about past ecosystems. However, several methodological challenges remain, particularly for classifying the DNA to species level and conducting phylogenetic placement. Current methods, primarily tailored for modern datasets, fail to capture several idiosyncrasies of aeDNA, including species mixtures from closely related species and ancestral divergence. We introduce soibean, a novel tool that utilises pangenomic graphs for identifying species from ancient environmental mitochondrial reads. It outperforms existing methods in accurately identifying species from multiple sources within a sample, enhancing phylogenetic analysis for aeDNA. soibean employs a damage-aware likelihood model for precise identification at low-coverage with high damage rate, demonstrating effectiveness through simulated data tests and empirical validation. Notably, our method uncovered new empirical results in published datasets, including using porpoise whales as food in a Mesolithic community in Sweden, demonstrating its potential to reveal previously unrecognised findings in aeDNA studies. ### Competing Interest Statement The authors have declared no competing interest.
Original URL: https://www.biorxiv.org/content/10.1101/2024.04.12.589157v1?med=mas
👍 Nikolay Oskolkov, Nicola Vogel, Louis Kraft, Aleksandra Laura Pach, Biancamaria Bonucci, Camila Duitama, Elena Zavala, Wenqin Yu, Mohamed Sarhan, Stephanie Dolenz, Benjamin Vernot, Liam Lanigan, Sterling Wright
Sterling Wright (sterlingwright2016@utexas.edu)
2024-04-23 17:33:41

Recent paper analyzing biomolecular data from Roman era individuals in Romania https://www.sciencedirect.com/science/article/pii/S2352409X2400138X

😮 Miriam Bravo, Biancamaria Bonucci
👍 Nikolay Oskolkov
🎉 Nikolay Oskolkov, Sarah Johnson
irinavelsko (irinavelsko@gmail.com)
2024-04-23 19:11:00

*Thread Reply:* Hi @Sterling Wright congratulations!

irinavelsko (irinavelsko@gmail.com)
2024-04-23 19:11:13

*Thread Reply:* Since the article isn’t open-access, would you mind sharing the pdf with us?

Sterling Wright (sterlingwright2016@utexas.edu)
2024-04-23 20:05:41

*Thread Reply:* Thank you and for sure! I hope this helps.

Wright-etal-2024-JAS-Reports.pdf
irinavelsko (irinavelsko@gmail.com)
2024-05-06 07:43:08

*Thread Reply:* Thanks!

🎉 Sterling Wright
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2024-05-14 09:13:50

Review from a Conor Meehan, who thinks the review might be of interest to us working on oral microbiomes/dental calculus

https://x.com/con_meehan/status/1790043501318537583

Paper: https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.001251

X (formerly Twitter)
Conor Meehan (@con_meehan) on X
Our oral microbiome evolution from ancient DNA data review is out! Led by @GDahlquistAxe and @fstandeven193 with @DrATedder and Camilla Speller, published in MGEN @MicrobioSoc and of interest to @spaam_community and others in microbiome evolution or aDNA. <https://t.co/0fdpZYpC8J>
Original URL: https://x.com/con_meehan/status/1790043501318537583
irinavelsko (irinavelsko@gmail.com)
2024-05-23 07:28:13

New preprint on diversity of oral Streptococcus in ancient dental calculus and modern oral samples from humans and non-human primates https://www.biorxiv.org/content/10.1101/2024.05.19.594849v1.abstract?%3Fcollection=

bioRxiv
Streptococcus abundance and oral site tropism in humans and non-human primates reflects host and lifestyle differences
The genus Streptococcus is highly diverse and a core member of the primate oral microbiome. Streptococcus species are grouped into at least eight phylogenetically-supported clades, five of which are found almost exclusively in the oral cavity. We explored the dominant Streptococcus phylogenetic clades in samples from multiple oral sites and from ancient and modern-day humans and non-human primates and found that clade dominance is conserved across human oral sites, with most species falling in the Sanguinis or Mitis clades. However, minor differences in the presence and abundance of individual species within each clade differentiated human lifestyles, with loss of S. sinensis appearing to correlate with toothbrushing. Of the non-human primates, only baboons show clade abundance patterns similar to humans, suggesting that a habitat and diet similar to that of early humans may favor the growth of Sanguinis and Mitis clade species. ### Competing Interest Statement The authors have declared no competing interest.
Original URL: https://www.biorxiv.org/content/10.1101/2024.05.19.594849v1.abstract?%3Fcollection=
:partyparrot: James Fellows Yates, Biancamaria Bonucci, Mohamed Sarhan, Marica Baldoni, Piotr Rozwalak, Florencia Alvarez Gallego, Yuejiao Huang, Nikolay Oskolkov, Bjorn Bartholdy, Jasmin Frangenberg, Aurore Galtier
aidanva (aida.andrades@gmail.com)
2024-06-30 10:25:53

Congratulations @Kadir Toykan Özdoğan ! https://link.springer.com/article/10.1007/s12520-024-01999-2

SpringerLink
Archaeology meets environmental genomics: implementing sedaDNA in the study of the human past
Archaeological and Anthropological Sciences - Sedimentary ancient DNA (sedaDNA) has become one of the standard applications in the field of paleogenomics in recent years. It has been used for...
Original URL: https://link.springer.com/article/10.1007/s12520-024-01999-2
❤️ Kadir Toykan Özdoğan, Zoé Pochon, Dawn lewis, Biancamaria Bonucci, Maria Lopopolo, Florencia Alvarez Gallego
👏 Mohamed Sarhan, James Fellows Yates, Zoé Pochon, Biancamaria Bonucci, Nasreen Broomand, Piotr Rozwalak
👏:skin_tone_6: Miriam Bravo
Meriam Guellil (meriam.guellil.ac@gmail.com)
2024-07-01 11:14:59

A bit of self promo but here is our preprint on the eleven first ancient HHV-6A and HHV-6B genomes 🥳 https://www.biorxiv.org/content/10.1101/2024.06.25.599715v1

:partyparrot: James Fellows Yates, Yuejiao Huang, Biancamaria Bonucci, Pooja Swali, Nikolay Oskolkov, Davide Bozzi, Matti Heino
🎉 Magdalena Haller-Caskie, Mohamed Sarhan, irinavelsko, Nikolay Oskolkov, Helja Niinemäe, Nasreen Broomand, Piotr Rozwalak, Louis L'Hôte
:meow_party: Zoé Pochon
:party_dino: Alina Hiss
❤️ Eugenia D'Atanasio, Katie McCormack, Biancamaria Bonucci
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2024-07-05 08:36:13

https://www.biorxiv.org/content/10.1101/2024.07.02.601727v1.full.pdf+html|https://www.biorxiv.org/content/10.1101/2024.07.02.601727v1.full.pdf+html

bioRxiv
Metagenomic peek into a corn mummy
Numerous studies have shown that metagenomics has opened up a new dimension in reading the contents of archaeological remains as time capsules. Corn mummies are ritual objects made in ancient Egypt by forming human-shaped figures made of cereal grains grown in a mixture of water and earth. We performed metagenomic analyses on samples from a corn mummy dated to the second half of the 3rd century BC. Alongside a number of clearly modern contaminants, we identified organisms that cannot be excluded as being of historical origin. Besides considerable amounts of bacterial sequences belonging to the genera Bacillus, Coprococcus, Metabacillus, Niallia and Roseburia, we also found traces of plants, animals, and humans. Sequences assigned to the genus Triticum showed the highest similarity to ancient T. turgidum ssp. dicoccum specimens from Egypt and the southern Levant. Sequences classified in the genus Populus showed the highest identity with the genome of P. nigra. The fragments that were identified as being of Lepidopteran origin showed the greatest similarity to the genomes of the Sphingidae. Haplotype analysis of H. sapiens sequences suggests haplogroups L3 and E, based on the mitogenome and Y chromosome, respectively, which are the two common lineages in sub-Saharan Africa today. ### Competing Interest Statement The authors have declared no competing interest.
Original URL: https://www.biorxiv.org/content/10.1101/2024.07.02.601727v1.full.pdf+html
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2024-07-05 08:36:24

Plant mummies?

🌽 Freya Steinhagen, Yuejiao Huang, Aleksandra Laura Pach, Ihini, aidanva, Luisa Sacristan