SPAAM

SPAAM Blog Post Competition · SPAAM Community Standards, Precautions, and Advances in Ancient Metagenomics

The SPAAM Community is thrilled to announce our first-ever blog post competition!
You will not only get a chance of having your post featured on the SPAAM website but also win a mystery book prize!
For more info and how to submit visit: www.spaam-community.org/news/2025/11...
#SPAAM #aDNA #contest

Thank you for bringing this to our attention! Fixed :)

Temporal succession of bacterial and archaeal communities in a Mediterranean high-mountain lake over the last 430 years using sedimentary DNA - Microbial Ecology Despite the known influence of climate change on high-altitude ecosystems, the long-term response of prokaryotic communities in Mediterranean high-mountain lakes remains poorly understood. Here, we…

Ancient microbe DNA as a record of climate change 🦠🧬: mountain lake sedaDNA from the past 430 years reveals major microbial shifts since 1960, following climate shifts.
doi.org/10.1007/s002...
#MetagenomicsMonday #SPAAM #aDNA #climate #change #metagenomics #sediment #sedaDNA #mountain #lake

How much do lab methods shape ancient microbiome results? 🧬 This study compares extraction & library prep protocols on dental calculus from Hungary and Niger, showing that no single workflow fits all. #MetagenomicsMonday #SPAAM #aDNA #calculus #microbiome
doi.org/10.1111/1755...

Improving taxonomic inference from ancient environmental metagenomes by masking microbial-like regions in reference genomes Abstract. Ancient environmental DNA is increasingly vital for reconstructing past ecosystems, particularly when paleontological and archaeological tissue r

This new study takes a closer look at eukaryotic reference genomes. 🧬 By mapping microbial-like regions across thousands of plant & animal assemblies, it helps make ancient eDNA analyses more accurate. #MetagenomicsMonday #SPAAM #aDNA #metagenomics #eDNA
doi.org/10.1093/giga...

🗳️🗳️Dear SPAAM community, have you voted for the SPAAM8 2026 meeting location yet?

The poll is open until Nov 22! Check Element General Room to choose your preferred option (Leipzig, Copenhagen, Stockholm, or online). Your input matters—help shape our next annual meeting!

Matrix - Decentralised and secure communication You're invited to talk on Matrix. If you don't already have a client this link will help you pick one, and join the conversation. If you already have one, this link will help you join the conversation

📣📣We’ve launched a new Introduction Room on our community Element channel! Whether you’re a new or veteran member, introduce yourself, share your affiliation, and tell us about your research. Let’s connect and strengthen our community together!

matrix.to#/#Introducti...

SPAAM Newsletter #7 Hello from the SPAAM Steering Committee!

Dear SPAAM Community members,
We are excited to share with you the latest SPAAM Newsletter!
Inside, you’ll find:
- updates on events and workshops
- funding/research opportunities
- latest publications
We hope you enjoy this edition!
www.spaam-community.org/assets/media...

Denisovan mitochondrial DNA from dental calculus of the >146,000-year-old Harbin cranium Denisovans have yet to be directly associated with a hominin cranium, limiting our understanding of their morphology and geographical distribution. We…

A new study links the Harbin cranium to Denisovans using DNA hidden in dental calculus. 🦷🧬 The mtDNA connects to Siberian lineages and suggests Denisovans spread widely across Pleistocene Asia. #MetagenomicsMonday #SPAAM #aDNA #Denisovan #archaic #mtDNA #calculus
doi.org/10.1016/j.ce...

Bone Adhered Sediments as a Source of Target and Environmental DNA and Proteins Abstract. In recent years, sediments from cave environments have provided invaluable insights into ancient hominids, as well as past fauna and flora. Unfor

In this new paper, researchers extended the sedaDNA analysis beyond cave sediments: bone-adhered deposits preserved human, microbial, plant & animal sequences. #MetagenomicsMonday #SPAAM #aDNA #sedaDNA #metagenomics #cave #sediment

ISBA11 Debriefing · SPAAM Community Standards, Precautions, and Advances in Ancient Metagenomics

Did you miss the ISBA11? Or maybe you want to refresh your memories from the symposium? 🧬 SPAAM members gathered for a debriefing session to share our impressions and feedback on the ISBA conference program. Check it out!
www.spaam-community.org/blog/2025/10...
#SPAAM #ancientDNA #ISBA11 #aDNA

Ancient microbial DNA and proteins preserve in concretions covering human remains Archaeological remains covered with concretions, including human bones, are commonly found in certain areas and time periods of interest for understan…

A new study explores the secrets hidden in concretions coating ancient teeth. 🦷 The researchers found microbial & protein traces, but human DNA remains elusive… #MetagenomicsMonday #SPAAM #aDNA #proteomics #metagenomics
doi.org/10.1016/j.is...

Many thanks to @jfy133.genomic.social.ap.brid.gy, @aidanva.bsky.social, Megan Michel, Cathy Tran, Yuejiao Huang, Lennart Schreiber, @christinawarinner.bsky.social, and @alexhbnr.bsky.social (🧵 4/4)

📈 More stats
🧬 2936 (+132) ancient host-associated metagenome libraries
🦠 3552 (+92) ancient microbial genome libraries
🌅 928 (+106) ancient environmental libraries
(🧵 3/4)

📈 Release v25.09.0:
📚 211 (+5) publications
🧬 1705 (+33) ancient host-associated metagenome samples
🦠 810 (+40) ancient microbial genomes
🌅 803 (+90) ancient environmental samples
(🧵 2/4)

Release v25.09: Site of Palmyra · SPAAM-community/AncientMetagenomeDir Release v25.09.0 includes 5 new publications, representing 33 new ancient host-associated metagenome samples, 40 new ancient microbial genomes, and 90 new ancient environmental samples. This brings...

🚨 New release of #AncientMetagenomeDir! (v25.09.0, Site of Palmyra)
github.com/SPAAM-commun...
It is a community resource of #metadata of >2K shotgun-sequenced #AncientMetagenome or ancient microbial genome enriched samples & >5K libraries. Stats below (🧵 1/4)

Many thanks to @jfy133.genomic.social.ap.brid.gy, @aidanva.bsky.social, Megan Michel, Cathy Tran, Yuejiao Huang, Lennart Schreiber, @christinawarinner.bsky.social, and @alexhbnr.bsky.social (🧵 4/4)

📈 More stats
🧬 2936 (+132) ancient host-associated metagenome libraries
🦠 3552 (+92) ancient microbial genome libraries
🌅 928 (+106) ancient environmental libraries
(🧵 3/4)

📈 Release v25.09.0:
📚 211 (+5) publications
🧬 1705 (+33) ancient host-associated metagenome samples
🦠 810 (+40) ancient microbial genomes
🌅 803 (+90) ancient environmental samples
(🧵 2/4)

Release v25.09: Site of Palmyra · SPAAM-community/AncientMetagenomeDir Release v25.09.0 includes 5 new publications, representing 33 new ancient host-associated metagenome samples, 40 new ancient microbial genomes, and 90 new ancient environmental samples. This brings...

🚨 New release of #AncientMetagenomeDir! (v25.09.0, Site of Palmyra)
github.com/SPAAM-commun...
It is a community resource of #metadata of >2K shotgun-sequenced #AncientMetagenome or ancient microbial genome enriched samples & >5K libraries. Stats below (🧵 1/4)

Proteomics + aDNA from a Jerash mass grave recovered Y. pestis genomes in 5 individuals. 🧬 Near-identical strains confirm a single lineage outbreak & place First Pandemic Y. pestis DNA near its historical epicenter. #MetagenomicsMonday #SPAAM #aDNA #plague #proteomics
doi.org/10.3390/gene...

What affects aDNA recovery from dental calculus? 🦷📊 In 32 mammal species, library success (~74%) was possibly shaped by host diet. #MetagenomicsMonday #SPAAM #aDNA

Interested in the past of reef organisms and ecosystems? 🪸 Sign up for the 2026 International Coral Reef Symposium that will take place in Auckland, NZ. The abstract submissions are open until December. #aDNA #SPAAM #ecosystems #reef #coral #symposium

A 75,000-y-old Scandinavian Arctic cave deposit reveals past faunal diversity and paleoenvironment | PNAS During the last glacial period (~118 to 11.7 ka), the Arctic has been characterized by a major redistribution of flora and fauna as a consequence o...

What lived in Arctic Norway ~80,000 years ago? ❄️🦌 Ancient sediments from a cave reveal 46 taxa of mammals, birds & fish — a unique cold-adapted coastal ecosystem. #MetagenomicsMonday #SPAAM #aDNA
doi.org/10.1073/pnas...

Bronze Age Yersinia pestis genome from sheep sheds light on hosts and evolution of a prehistoric plague lineage Most human pathogens are of zoonotic origin. Many emerged during prehistory, coinciding with domestication providing more opportunities for spillover …

Did prehistoric sheep carry plague? 🐑🦠 A 3rd-millennium BCE Yersinia pestis genome from domesticated sheep links livestock to human infections in prehistory. #MetagenomicsMonday #SPAAM #aDNA
doi.org/10.1016/j.ce...

Ancient host-associated microbes obtained from mammoth remains Ancient genomic studies have extensively explored human-microbial interactions, yet research on non-human animals remains limited. In this study, we a…

What can a million-year-old mammoth teach us about microbes? 🦠 From pathogens to commensals, this new study reconstructs the oldest known host-associated microbial DNA. #MetagenomicsMonday #SPAAM #aDNA
doi.org/10.1016/j.ce...

#MetagenomicsMonday A new study shares 174 archaeological dental calculus metagenomes from across the UK, spanning multiple periods. With rich metadata and rigorous quality control, the dataset opens new doors to exploring ancient microbiome through time.
doi.org/10.1016/j.di...

SPAAM Summer School (2025): Introduction to Ancient Metagenomics Share your videos with friends, family, and the world

Interested in learning more about how researchers analyze ancient DNA? Here you can find the free lectures from the SPAAM Summer School 2025 - Introduction to Ancient Metagenomics: tinyurl.com/3u9mhmd2
Slides: tinyurl.com/mkfrvru4
Feel free to ask questions in the comments!
#ancientDNA #SPAAM

#MetagenomicsMonday Are you interested in ancient microbiome and sedaDNA? Check out wholeskim - new fast and efficient pipeline that uses unassembled genome skims to index and query k-mers for taxonomic annotation of environmental DNA.
onlinelibrary.wiley.com/doi/10.1111/...

Our wonderful speakers:
@aidanva.bsky.social
@davidebozzi.bsky.social
Yuejiao Huang
@zoepochon.bsky.social
Keri Burge
Katherine Hearne
Marcel Keller
@jmuurine.bsky.social
Madeleine Thirolle
@bbonucci.bsky.social
@giuliazamp93.bsky.social
@anthbyte.bsky.social