SPAAM Newsletter #7

• Announcements
• Brief overview of recent events
• Upcoming Physalia courses
• Job announcements
• Funding opportunities
• Recent publications
• Publication highlights

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Announcements

SPAAM Instagram 📷

SPAAM officially launched an Instagram account!

Our Instagram is a space to connect with our community and introduce our activities/members to the wider public.

If there is anything you would like to appear on the IG account, please submit them using this form. We are also looking for any photos or graphics from members to support future posts!

We are still looking for volunteers to help us run the IG account. So, if you are interested please reach out to the Media Team at spaam.community@gmail.com

Connect with us on Instagram @spaamcommunity!

SPAAM Blog 📝

Our blog is looking for new contributions! You want to explain a concept in ancient metagenomics that is often misunderstood? Would you like to introduce a new methodology or pipeline to the wider community? You attended a conference or workshop recently and would like to share your impressions? Please get in touch with Marcel Keller (marcel.keller@unibas.ch or on Element) or any other member of the Steering Committee with your idea.

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Brief overview of recent events

SPAAM 7

The day before ISBA11, the SPAAM Community held the SPAAM7 meeting in Turin. Over 40 people attended in person and 50 joined SPAAM7 virtually to listen to six full talks and three flash talks.

During this satellite meeting, our members shared their exciting research and discussed ongoing efforts to improve authentication practices, metadata standards, and data accessibility in ancient metagenomics.

ISBA 11

The biggest ISBA yet, with 570 attendees, ISBA11 took place in Turin, Italy – a charming town that blends royal heritage, baroque architecture, and a vibrant food and café culture.

Over four days, the program showcased the breadth of our field, with sessions on ancient DNA, palaeoproteomics, lipids, isotopes, diet and foodways, mobility and migration, palaeopathology, human–environment interactions, and exciting new methodological advances.

Keynote talks set the stage for stimulating conversations, while panels and round tables encouraged thoughtful reflection on ethics, equity, and sustainability in biomolecular archaeology.

Beyond the science, ISBA11 had a wonderfully collegial atmosphere, providing a chance to reconnect with familiar faces, meet new colleagues, and spark fresh collaborations, all while enjoying the cultural setting (and excellent food!). It was a truly memorable meeting that highlighted just how vibrant and connected our community has become.

Couldn’t join us in Turin? The keynote talks are now available for everyone to watch:

• Joanna Brück
• Cristina Valdiosera
• Shinya Shoda
• Enrico Cappellini
• Judy Sealy

The SPAAM Community is already looking forward to ISBA12 and hoping to see you there!

Introduction to Metagenomics Summer School 2025

This year, the SPAAM Community led the 4th edition of Introduction to Ancient Metagenomics Summer School in collaboration with the Max Planck Institute for Evolutionary Anthropology, Friedrich Schiller Universität Jena, and Harvard University.

The main steps of ancient metagenomic bioinformatic workflows were taught by an amazing group of experienced volunteer instructors from multiple institutions. The students learned how to use the command line, process next-generation-sequencing data, and more!

If you missed this year’s Summer School, do not worry! You can still gain free access to the video lectures and learn how to process and analyze your own ancient metagenomic data! 🎓

Upcoming Physalia courses

• Environmental Metagenomics
  13-17 October
  This course provides hands-on training in state-of-the-art bioinformatic approaches for metagenomic analysis, focusing on read- and assembly-based methods and the use of short- and long-read sequencing to recover metagenome-assembled genomes (MAGs) from complex microbial communities.

• Population Genomic Inference From Low-Coverage WGS Data
  20-23 October
  This course introduces participants to probabilistic frameworks and best-practice workflows for analyzing low-coverage sequencing data in population genomics, focusing on methods implemented in ANGSD and related tools.

• Museomics
  3-7 November
  This course offers an introduction to museomics, combining lectures and practical exercises to teach essential bioinformatics workflows and analytical methods for generating and analyzing genomic data from natural history collections.

• Shotgun Metagenomics Processing And Analysis
  25-28 November 2025
  This course provides a comprehensive introduction to advanced bioinformatics methods for shotgun metagenomics, combining lectures and hands-on practice to train students in data preprocessing, taxonomic and functional profiling, genome reconstruction, statistical analysis, and result visualization.

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Job announcements

Postdoc

• Archaeogenetic analyses of domestic sheep from the Iberian Peninsula and North Africa. CIBIO-InBIO, in Vairão, Vila do Conde, Portugal

• Medieval stećci tombstones in the Western Balkans. Research Centre of the Slovenian Academy of Sciences and Arts, Slovenia

• Ancient pathogen genomics. UCL, London, UK

• Population genetics and natural selection in Central Eurasia, University of Texas in Austin, USA

• Population genetics of humans and sheep at Uppsala University, Sweden

• Marine and environmental aDNA, Geological Survey of Denmark and Greenland (GEUS)

• Ancient pathogen genomics, MPIIB, Berlin, Germany

• Experimental environmental aDNA, CSIRO, Australia

PhD

• ERC Project HERDPATH - livestock and pathogen co-evolution - deadline: 3rd Oct 2025, University College Dublin, UK

• Ancient environmental genomics, University of Vienna, Austria

• The “Disperse” ERC project will explore the key steps in the movement of humans out of Africa and into Eurasia

Tenure-track

• Assistant Professor in Biological Anthropology at Tulane University, USA

• Assistant Professor in Biological Anthropology at University of Oklahoma, USA

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Funding opportunities

PhD Studentships

• EMBL International PhD Programme - deadline 13 Oct 2025

Postdoctoral Fellowships & Grants

• EMBO Postdoctoral Fellowships: applications accepted all year-round, international mobility required.

• Wellcome Early-Career Awards: deadline - 30 Sept 2025

• The British Academy Postdoc Fellowships (UK): deadline - 1 Oct 2025

• Postdoctoral Fellowship in Toulouse, France: deadline - 15 Nov 2025

• Provost Postdoctoral Fellowship at the University of Notre Dame, USA

Small Grants

• EMBO Scientific Exchange Grant: on a rolling basis, for 1-3 months of exchanges in EMBC countries

• Leverhulme Small Research Grants (UK): deadline - 5 Nov 2025, up to 10k pounds for focused projects

• The Explorers Club - Pathfinder Grant: deadline - 8 Oct 2025, 2.5-5k USD for fieldwork

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Recent publications

Adapa et al., Genetic Evidence of Yersinia pestis from the First Pandemic

Augias et al., An ancient Epstein-Barr virus genome recovered from a museum penis gourd from Papua

Boast et al., Long-term parasite decline associated with near extinction and conservation of the critically endangered kākāpō parrot

Bonucci et al., Ancient microbial DNA and proteins preserve in concretions covering human remains

Campbell et al., Using sedimentary ancient DNA in coastal and marine contexts to explore past human–environmental interactions in Australia

de-Dios et al., Bone adhered sediments as a source of target and environmental DNA and proteins

Elliott et al., wholeskim: Utilising Genome Skims for Taxonomically Annotating Ancient DNA Metagenomes

Fagin et al., Parasite sedimentary DNA reveals fish introduction into a European high-mountain lake by the seventh centurys

He et al., Thousands-years-old deep-sea DNA viruses reveal the evolution of human pathogenic viruses

Holman et al., Ancient environmental DNA indicates limited human impact on marine biodiversity in pre-industrial Iceland

Kuldeep et al., Validating a Target-Enrichment Design for Capturing Uniparental Haplotypes in Ancient Domesticated Animals

Ledger et al., Sedimentary ancient DNA as part of a multimethod paleoparasitology approach reveals temporal trends in human parasitic burden in the Roman period

Lévêque et al., Hiding in plain sight: the biomolecular identification of pinniped use in medieval manuscripts

Light-Maka et al., Bronze Age Yersinia pestis genome from sheep sheds light on hosts and evolution of a prehistoric plague lineage

Mascarenhas et al., Widespread occurrence of botulinum and tetanus neurotoxin genes in ancient DNA

Moraitou et al., Host Traits Impact the Outcome of Metagenomic Library Preparation From Dental Calculus Samples Across Diverse Mammals

Noda et al., Ancient DNA integrates fossil and modern giant salamander taxonomy

Schreiber et al.,Holocene shifts in marine mammal distributions around Northern Greenland revealed by sedimentary ancient DNA

Sikora et al., The spatiotemporal distribution of human pathogens in ancient Eurasia

Standeven et al., An extensive archaeological dental calculus dataset spanning 5000 years for ancient human oral microbiome research

Swali et al., Ancient Borrelia genomes document the evolutionary history of louse-borne relapsing fever

Walker et al., A 75,000-y-old Scandinavian Arctic cave deposit reveals past faunal diversity and paleoenvironment

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Publication highlights

In this edition of Publication Highlights, we want to shed light on two fascinating articles that were recently published in Science and Cell!

Pre-European contact leprosy in the Americas and its current persistence

Lopopolo et al. (2025) Science

Leprosy is caused by two pathogens: Mycobacterium leprae (long studied and linked with European colonization of the Americas) and Mycobacterium lepromatosis (only identified in 2008, mainly reported in the Americas today). Until now, the evolutionary and epidemiological history of M. lepromatosis has been almost completely unknown.

Lopopolo et al. bring aDNA into the spotlight by showing that leprosy caused by M. lepromatosis was present in the Americas centuries before European arrival.

The team:

• Generated a high-quality de novo reference genome of M. lepromatosis from a Costa Rican strain, using long-read sequencing for improved resolution.

• Screened 408 modern clinical samples from five American countries, identifying 34 positive cases and reconstructing 24 genomes.

• Screened 389 ancient samples and identified M. lepromatosis DNA in three individuals from Canada and Argentina (dated 860–1310 BP), providing definitive pre-contact evidence in both North and South America.

• Reconstructed the pathogen’s evolutionary history, revealing five major clades. Two were defined by the ancient American strains, while another basal lineage diverged ~10,000 years ago.

• Traced modern connections, showing that the red squirrel clade in the British Isles likely has an American origin, expanding during the 19th century.

These results re-estimate the divergence between M. leprae and M. lepromatosis to 2 million–700,000 years ago (far more recent than the previously assumed ~14 million years) and demonstrate that several M. lepromatosis clades diversified in the Americas during the Late Holocene, some of which persist today.

💡 This is a landmark study showing how aDNA reshapes our understanding of neglected pathogens: leprosy in the Americas was not just introduced by Europeans as it had its own complex, endemic history long before contact!

Ancient host-associated microbes obtained from mammoth remains

Guinet et al. (2025) Cell

Ancient DNA has revealed a great deal about past human–microbe interactions, but non-human hosts have remained largely unexplored.

Guinet et al. push the boundaries by analyzing microbial DNA from 483 mammoth remains spanning more than a million years, including data from a 1.1-million-year-old steppe mammoth.

The team:

• Screened 483 mammoth samples (440 newly sequenced) using metagenomics, contaminant filtering, and damage authentication.

• Identified 310 microbial taxa associated with mammoth tissues, most of which were environmental or post-mortem colonizers.

• Recovered genomic evidence of six persistent host-associated clades (including Actinobacillus, Pasteurella, Streptococcus, and Erysipelothrix) that spanned both regions and time periods.

• Detected putative virulence factors in some lineages, including a Pasteurella-related bacterium previously implicated in elephant die-offs.

• Reconstructed partial genomes of Erysipelothrix from the 1.1-million-year-old steppe mammoth - the oldest authenticated host-associated microbial DNA recovered to date!

💡 This study demonstrates that mammoth remains can serve as microbial archives, opening up new avenues to explore the health, ecology, and co-evolution of extinct megafauna through ancient DNA.