SPAAM
@spaam-community.bsky.social
We are a community of researchers focusing on standards, precautions, & advances in ancient #metagenomics (SPAAM)
https://www.spaam-community.org/
https://www.spaam-community.org/
Recovering DNA from ancient plants is tough, but this new method makes it work! A new extraction workflow improves recovery of fragmented endogenous plant aDNA while preserving library complexity and read yield.
www.nature.com/articles/s41...
#MetagenomicsMonday #SPAAM #aDNA #archaeobotany
www.nature.com/articles/s41...
#MetagenomicsMonday #SPAAM #aDNA #archaeobotany
Optimizing ancient DNA recovery from archaeological plant seeds - Scientific Reports
Scientific Reports - Optimizing ancient DNA recovery from archaeological plant seeds
www.nature.com
December 8, 2025 at 7:45 AM
Recovering DNA from ancient plants is tough, but this new method makes it work! A new extraction workflow improves recovery of fragmented endogenous plant aDNA while preserving library complexity and read yield.
www.nature.com/articles/s41...
#MetagenomicsMonday #SPAAM #aDNA #archaeobotany
www.nature.com/articles/s41...
#MetagenomicsMonday #SPAAM #aDNA #archaeobotany
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
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
SPAAM Blog Post Competition · SPAAM Community
Standards, Precautions, and Advances in Ancient Metagenomics
www.spaam-community.org
December 3, 2025 at 1:42 PM
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
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
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
doi.org/10.1007/s002...
#MetagenomicsMonday #SPAAM #aDNA #climate #change #metagenomics #sediment #sedaDNA #mountain #lake
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…
doi.org
December 1, 2025 at 8:01 AM
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
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...
doi.org/10.1111/1755...
November 17, 2025 at 8:01 AM
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...
doi.org/10.1111/1755...
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...
doi.org/10.1093/giga...
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
doi.org
November 10, 2025 at 8:01 AM
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...
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!
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!
November 7, 2025 at 3:49 PM
🗳️🗳️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!
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!
📣📣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...
matrix.to#/#Introducti...
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
https://matrix.to/#/#Introductions:matrix.org
November 7, 2025 at 3:03 PM
📣📣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...
matrix.to#/#Introducti...
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...
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...
SPAAM Newsletter #7
Hello from the SPAAM Steering Committee!
www.spaam-community.org
November 7, 2025 at 2:55 PM
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...
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...
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...
doi.org/10.1016/j.ce...
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…
doi.org
November 3, 2025 at 8:01 AM
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...
doi.org/10.1016/j.ce...
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
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
doi.org
October 27, 2025 at 8:02 AM
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
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
www.spaam-community.org/blog/2025/10...
#SPAAM #ancientDNA #ISBA11 #aDNA
ISBA11 Debriefing · SPAAM Community
Standards, Precautions, and Advances in Ancient Metagenomics
www.spaam-community.org
October 24, 2025 at 3:58 PM
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
www.spaam-community.org/blog/2025/10...
#SPAAM #ancientDNA #ISBA11 #aDNA
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...
doi.org/10.1016/j.is...
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…
doi.org
October 20, 2025 at 7:01 AM
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...
doi.org/10.1016/j.is...
🚨 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)
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)
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...
github.com
October 17, 2025 at 1:39 PM
🚨 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)
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)
🚨 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)
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)
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...
github.com
October 17, 2025 at 12:20 PM
🚨 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)
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...
doi.org/10.3390/gene...
doi.org
October 13, 2025 at 7:02 AM
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...
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
doi.org
October 6, 2025 at 7:01 AM
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
September 29, 2025 at 1:04 PM
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
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...
doi.org/10.1073/pnas...
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...
doi.org
September 29, 2025 at 7:02 AM
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...
doi.org/10.1073/pnas...
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...
doi.org/10.1016/j.ce...
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 …
doi.org
September 22, 2025 at 7:01 AM
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...
doi.org/10.1016/j.ce...
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...
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…
doi.org
September 15, 2025 at 7:36 AM
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...
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...
doi.org/10.1016/j.di...
An extensive archaeological dental calculus dataset spanning 5000 years for ancient human oral microbiome research
Archaeological dental calculus can provide detailed insights into the ancient human oral microbiome. We offer a multi-period, multi-site, ancient shot…
doi.org
September 8, 2025 at 7:36 AM
#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...
doi.org/10.1016/j.di...
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
Slides: tinyurl.com/mkfrvru4
Feel free to ask questions in the comments!
#ancientDNA #SPAAM
SPAAM Summer School (2025): Introduction to Ancient Metagenomics
Share your videos with friends, family, and the world
tinyurl.com
September 2, 2025 at 12:57 PM
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
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/...
onlinelibrary.wiley.com/doi/10.1111/...
onlinelibrary.wiley.com
September 1, 2025 at 7:01 AM
#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/...
onlinelibrary.wiley.com/doi/10.1111/...
A huge thanks to all the amazing speakers and participants at #SPAAM7 yesterday 🧬🙌
The sessions were full of inspiring talks and great discussions!✨
The sessions were full of inspiring talks and great discussions!✨
August 27, 2025 at 3:45 PM
A huge thanks to all the amazing speakers and participants at #SPAAM7 yesterday 🧬🙌
The sessions were full of inspiring talks and great discussions!✨
The sessions were full of inspiring talks and great discussions!✨
Davide Bozzi shared results from his study of Aboriginal Australian saliva microbiomes, revealing a high diversity of novel species🦠
Follow him for more insights!
@davidebozzi.bsky.social
#SPAAM7 #aDNA
Follow him for more insights!
@davidebozzi.bsky.social
#SPAAM7 #aDNA
August 26, 2025 at 9:25 AM
Davide Bozzi shared results from his study of Aboriginal Australian saliva microbiomes, revealing a high diversity of novel species🦠
Follow him for more insights!
@davidebozzi.bsky.social
#SPAAM7 #aDNA
Follow him for more insights!
@davidebozzi.bsky.social
#SPAAM7 #aDNA