Hi friends! Anyone flying into Talinn on the 19:20 flight from Helsinki on Monday?

:spamdance: :spamdance: :spamdance: :spamdance: :spamdance: :spamdance: :spamdance: :spamdance: :spamdance: :spamdance:

Welcome everyone! Here is a small channel to discuss anything related to the SPAAM5 meeting in Tartu 😊. The other organisers and myself are looking forward to seeing you there! 🥳

Hi everyone! We are happy to share with you the program for SPAAM5!! :spaam:🎉:party_dino: The meeting will be taking place in-person in Tartu (Tartu Nature House, Lille 10 Tartu 51010, Estonia), on September 12, 2023. We are looking forward to an exciting day featuring the presentation of multiple SPAAM projects and initiatives, flashtalks, discussions, and just getting to know each other. We will also be sending the program around via email later today.

SPAAM5 In-Person Meeting - Program.pdf

@channel For those of you who haven’t already done so, we would like to remind you to please pay the £15 registration fee. See you next week at SPAAM5!

Do we have any requiremetns in presentation formats?

Will there be a computer for us to upload our talks to? Or do we need to use our own computer?

There will be a computer to upload the presentation to and if you are using google slides you can send us the link whenever you are ready

Hi all, can someone remind me where we're meeting tomorrow? Because it's not at the museum, right?

Sorry - I'll be a bit late this morning (missed my coach from Tallinn 🥲) is there a specific room we are in and anywhere I can puy my luggage when I get there?

Follow this link to join my WhatsApp group: https://chat.whatsapp.com/ILv7546ijM3GDRieZzBlYK

WhatsApp.com

SPAAM5 Funsies

WhatsApp Group Invite

Original URL: https://chat.whatsapp.com/ILv7546ijM3GDRieZzBlYK

If you don't have slack on your phone but want to keep on contact e.g. for arranging social stuff/help etc the WhatsApp group is for SPAAM5 and isba

Any other ancientmetagneomiclabs updates? Please let me know on <#C02CZ8J898V|ancient-metagenomics-labs>

Group 3: https://hackmd.io/@jfy133/ByqC7i60n

Title: "Why do we use that mapper? I dunno 🤷‍♂️️ because pop-gen do it?"

Group 1

No one has really done sequencing, we usually let someone else do it (within the organisation or an external service) and we’re not very familiar with the process in detail With development of flow cells there is some concern about contamination if we’re not separating lanes as previously. Be strict about index matching. Insert barcodes that are specific to a lab? Pain in ass for bioinformatics to add a step after cutting adapters where we cut out the barcode, but maybe they can be improved

Contamination Sequencing blanks - sequencing reagents to find contaminants, there’s a study from 2014? - another one would be useful Human, burkholderia.

Quality control Removing reads under 30bp is a standard fastqc is a standard approach - but what are we looking for? This can sometimes be confusing Checking that adapters are removed Separating human and microbial data, Eager, bbmerge

Classifiers People have been struggling getting heavy classifiers to work, if you don’t have a bioinformatics background it’s hard to get some things to work (aMeta, nfcore, eager, even MALT)

MALT/HOPS Ignore edit distance when looking at viruses

Metaplan4 includes mags now (yay) Good for looking for community? Oral microbiome Curated database Only markers so might be missing stuff Human biased database - great if you work with humans

Kraken2/unique good for viral DNA HBV - kraken works better - edit distance means it doesn’t make past HOPS Viruses in general (Pavian - visual tool for Kraken)

aMETA - combination of Kraken and mapping

metaDamage - looks for damage patterns

Blast

Haystack Good for animals?

Magnify database Good for animals

GBTK Based on average nucleotide identity Can use mags Nice when looking at bacteria Not so much for eukaryotes or viruses Not directly comparable to NBCI taxon ID : Seqtk - to make it compatible

Contaminator - Table with known contamination Patric Database Pathogensportal.org

Conclusions: Superior method? aMeta?? Looks promising - needs benchmarking Look into graph database - store variation in a graph - compact database : meta graph <- way to go in the future?

Table 5 - Validation of Presence Google doc - please add any insight https://docs.google.com/document/d/1zmQ8Eb7Lx0l1RmsXD3Jm4b9pMQDoNb7O/edit?usp=sharing&ouid=109368001758301026751&rtpof=true&sd=true

Group 6. Authentication discussion session notes

Three main points:

1. Dynamic, fluid decision process on a sample-by-sample and site-by-site basis

-Is actually target microbe? Breadth of coverage Depth of coverage Blank analysis Validate with capture Competitive mapping to genus

-Is ancient? Need to have enough reads to get consistent results! Deamination patterns as first look is usually best Fragment length, especially if deamination is not the best Phylogenetic placement can be useful, especially with control samples Blank analysis MetaDamage useful -> raw sequencing reads get blasted and then damage calculated for best hits can be good for characterizing overall damage of a given sample metagenome

2. Uncharacterised range of variation Among organisms Within archaeological sites Within burial environments

Variation in authentication metrics can be high and doesn’t necessarily signal contamination

3. Little science done on the processes that result in fragmentation and damage accumulation and how the burial and storage environments contribute to the rate of these processes

Group 6: Ethical considerations in ancient metagenomics notes: https://hackmd.io/@jfy133/SyWY_06A2/edit

hackmd.io

SPAAM5 Ethics Discussion - HackMD

Original URL: https://hackmd.io/@jfy133/SyWY_06A2/edit

Discussion 2 - Group 2 - pathogens Skeletal clues to infection - try to sample the bone if there is a lesion but otherwise use teeth mainly. Sometimes we get “the leftovers” from human demography - everything is shotgun sequenced with no targeting Capture - UDG vs non-UDG treated - no smiley plots - UDG half to get indications of damage Single stranded

Classifier - MALT is not as useful for viral DNA RNA - no one has worked with it - there are no proper tools - “when the tool comes I’ll use it”

Pathogen - how bad is the disease? Did it affect the host

Soil samples to detect contamination should be done more

Authentication - are we getting more false positives or false negatives? Flag species that are problematic - pathogens that come up in everyones samples

Discussion 3 - oral microbiome Problems • database curation • biases (e.g. genome sizes) • identifying calculus, especially in animals • contamination estimation/decontamination (tools)? ◦ soil samples as comparison ◦ frontal part of the cranium as control ◦ sourcetracker, metasourcetracker, decontam ◦ batch effects: check for blanks, index hopping Topics • antimicrobial resistance in lifestock • sequencing strategy: screening for contamination check and deeper sequencing • Classifiers: Kraken, Bracken, metaPhlAn, HuMAnN • strain-level analyses: ◦ e.g. for phylogenetics ◦ check for heterogeneity first • extraction protocols: EDTA+PK • wet-lab decontamination ◦ bleach with wash ◦ UV light • viruses: retrievable from calculus • eukaryotic DNA: difficult to authenticate • differential sampling (different teeth of the same individual): probably less important, but sampling place should be reported

Discussion Group 1 offshoot - an outdoor rambling chat on sedaDNA How can we predict what sites / areas will work well for analysing ancient DNA from sediments? • Can it be linked to bones? • pH / temperature / time are all important factors • There will be a talk at ISBA for it (Merlin Szymanski) Thoughts on different soil types • Peat bogs are challenging • Sandy – not at the moment, but maybe some day! • Clay is good • Cold environment helps; permafrost is good Sampling strategies • Bottom up! • Falcon tubes are often used • It can be good to take samples above and below the layer of interest • A project might be undertaken in the future to compare different approaches Extraction methods • There are a variety of protocols across different groups – it isn’t streamlined • Approaches can depend on the type of sediment – but no trends for characteristics (eg phosphate extraction) protocols to make things more streamlined • Soil inhibition is still an issue • Can be explored using the 1) spike test or 2) dilution test • Soil / Easy Kit is good – you can go up to 5gs with it (a lot)

i have to leave early but it was wonderful day with you all !

❤️

Town hall notes: https://hackmd.io/@jfy133/S1Tbv1ACh

Please can some volunteer to take notes!

HackMD

SPAAM5 - HackMD

Marcel Q: What are plans for integrating SPAAM into ISBA

Original URL: https://hackmd.io/@jfy133/S1Tbv1ACh

@James Fellows Yates has a polly for you!

EAA: European Archaeological Association ISBAL INternational soceity for Biomoecular archaelogy SMBE: Society for Molecublar Bioloar and evolution AABA: American Associ. Biological Atnh. SAA: Scientific of American Archaeology

May I just say how beautiful today's SPAAM5 was? Really perfect organisation (we forgot to cheer for the committee!), thank you very much for that! 👏It was great fun to participate and discuss with all of you. And also the location choice, I loved the cozy Nature House (and the turtles in the green house of course 🐢). Thank you all and see you tomorrow at ISBA10!

Fully agree with Jasmin! Thank you so much the SPAAM5 organizing committee (and our common ancestor James 🙂) for the fantastic job! ❤️ 👏

We do post social event pictures here, right? Cheers from the climbing crew (ronimismeeskond) :vikingparrot:

spaam5_boulder_crew.jpg

(posted in wrong channel yesterday 🫠) Discussion 2 phylogenetics

Two approaches

1. SNP alignment -Map to your reference -Call and filter variants -Generate a multiple sample SNP alignment (MultiVCFAnalyzer, custom script) Use the resulting fasta file in your tree inference tool of choice

2. Gene tree See https://github.com/maxibor/corephylo -Make and bin contigs -Include your contigs and your referece genomes as input fastas -Annotate your contigs -Core genome generation -Remove recombinant regions -Treeeeeees!

ML tree inference IQtree easy and very good tutorial RAxML

Bayesian tree inference BEAST, BEAST2 for time trees RevBayes as an alternative

Fast and dirty tree inference FastTree

Downsampling and trimming Treemer to downsampling for more efficient tree building ClipKIT to trim regions that are not phylogenetically informative (reduces width of input data)

Visualization: FigTree http://tree.bio.ed.ac.uk/software/figtree/ ITOL https://itol.embl.de/ ggtree (R) https://github.com/YuLab-SMU/ggtree Icy tree (https://icytree.org/)

@Yi Wang at ISBA10!

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@Nikolay Oskolkov at ISBA10!

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Also @Biancamaria Bonucci hosting the session repping her SPAAM5 T-Shirt (but can't get a photo of her without a pedestal or someones head in the way)

@Liam Lanigan at ISBA10!

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@Ian Light at ISBA10!

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@James Fellows Yates at ISBA10!!!! 🔥

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@Oya Inanli at ISBA10!! 🍻

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@Iseult at ISBA10!!

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@Gunnar Neumann at ISBA10!

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Damn the community have quite a few talks actually!

Good job everyone 👏

And even more!

@Aleksandra Laura Pach at ISBA10!

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https://web.polly.ai/vdbpgv @channel are you interested to meet for a #spaamtisch chit chat on your fav ISBA10 talks? Go vote on the channel!

Also, PIs are invited to join the fun 🙂 we want to know all your positive takes on the talks and posters 🙂

Yes, I would post this in general. Almost only the spaam5 attendees are in this channel

Ah okay sorry 😅🙈

Hello! For the people at #ISBA10. We are having a #spaamtisch de-briefing of #ISBA10. Topic: which were your favorite talks and why? When: from 15 to 15:30 Where:Helmi Kurrik Lecture Hall

PIs join us! We want to have your positive takes on all the students' talks and posters!

See you there!

P.S. the meeting it's very informal!

Soooooo apparently the bingo remembered I was playing this since the last ISBA

Hi @channel for everyone who's interested in a big lab extraction/library protocol test like we discussed at the meeting last week, head over to <#C01BJPKHH9P|lab-community> if you're not already there to join the discussion!

heya @Meriam Guellil @Alina Hiss @Sierra Blunt @Zoé Pochon @Megan Michel -- thanks again for organizing such a great conference. I (and probably others) need to have a certificate of attendance at SPAAM for travel reimbursement/credit point purposes. Do you think you could make one for me and send me one? Thanks in advance !! 🙂

Hi everyone! Sorry we haven't had a new meeting yet and still need to deal with that. Do we have a SPAAM template for official documents? Or examples from last year?

Everyone who needs a certificate of attendance, leave a thumb up on this message please (we have been contacted in so many different ways that it's hard to keep track 😅)

SPAAM5 certificates have been sent out! 😊

Thanks again everyone for attending 😎

Thank you to the SPAAM5 organisers and attendees for a FANTASTIC first in-person SPAAM event, I was highly impressed by the quality of the organisation as well as the all the talks and discussions 🎉

👏 👏 👏 👏 👏 👏 👏 👏 👏 👏 👏 👏 👏 👏 👏 👏 👏 👏 👏 👏 👏 👏 👏 👏 👏 👏 👏 👏 👏 👏 👏 👏 👏

The steering committee will get in touch with the provisional SPAAM6 organisation team soon!

Did I miss where did we post the group picture from the stairs of the Nature House? Cannot find it 👀

Hello all!

We are excited to announce the SPAAM5 online event of the term, SPAAM5 Part 2!

We hope that everyone who attended SPAAM5 in Tartu had a great time! Now, as promised, the time has come for the SPAAM5 online event, “SPAAM5 Part 2” which will be held on Tuesday and Wednesday, January 30 and 31, 2024 on Zoom. So it is time to submit abstracts! Please submit an abstract of a maximum of 200 words to https://docs.google.com/forms/d/e/1FAIpQLSdIK2du4nfRi1p5aLJSCMFUrG4hgp1JwE2Ne1lgAZiaXYLNRw/viewform?usp=sharing by 11:59pm CET on November 30th. We would like to particularly encourage people who were unable to attend the SPAAM5 in person meeting to submit. This is a great opportunity to hear about amazing new research from young investigators across the globe without any limitations set by travel or budget. We will try to accommodate time zones wherever possible, so that more people can participate, as was the case with the previous online version of SPAAM. Principal investigators are welcome to participate in this edition, but are politely asked to leave sufficient space for early-career researchers during the discussions. If you submit an abstract, please plan for a presentation in the form of a 10-minute talk followed by 3 minutes of questions. There is no registration fee. Thanks very much and we look forward to your submissions!

Welcome to the second part of Standards, Precautions, and Advances in Ancient Metagenomics, edition 5!

Sincerely, SPAAM5 Organizers (Meriam Guellil, Zoé Pochon, Alina Hiß, Alice Lee, Sierra Blunt, and Megan Michel)

Hello all,

As Zoé mentioned last week, the organization of SPAAM5 Part 2 is officially underway! This event will be held virtually in order to accommodate the entire SPAAM community. If you attended the in-person meeting in September, we would love your feedback. What did or didn't work for you? What would you like to see at our next meeting? Please share your thoughts with us by filling out this anonymous survey before Friday, November 17th: https://forms.gle/QMF2fvphn5QBc8QC8

Thank you! SPAAM5 Organizers (Alice, Alina, Megan, Meriam, Sierra, and Zoé)

Hey everyone! When making the discussion tables for SPAAM5-onsite in Tartu, I recall we had a table for both sedaDNA and eukaryote metagenomics and we had to split the table as there was too many people. Could you maybe develop a bit for me what you consider to be eukaryote metagenomics? We’re looking for people with expertise in the different aspects of ancient metagenomics for an FAQ and I would need to have a clearer picture of that research field