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Ancient host-associated microbes obtained from mammoth remains

Guinet, Benjamin ; Oskolkov, Nikolay LU ; Moreland, Kelsey ; Dehasque, Marianne ; Chacón-Duque, J. Camilo ; Angerbjörn, Anders ; Arsuaga, Juan Luis ; Danilov, Gleb ; Kanellidou, Foteini and Kitchener, Andrew C. , et al. (2025) In Cell 188(23). p.24-6619
Abstract

Ancient genomic studies have extensively explored human-microbial interactions, yet research on non-human animals remains limited. In this study, we analyzed ancient microbial DNA from 483 mammoth remains spanning over 1 million years, including 440 newly sequenced and unpublished samples from a 1.1-million-year-old steppe mammoth. Using metagenomic screening, contaminant filtering, damage pattern analysis, and phylogenetic inference, we identified 310 microbes associated with different mammoth tissues. While most microbes were environmental or post-mortem colonizers, we recovered genomic evidence of six host-associated microbial clades spanning Actinobacillus , Pasteurella , Streptococcus, and Erysipelothrix . Some of these clades... (More)

Ancient genomic studies have extensively explored human-microbial interactions, yet research on non-human animals remains limited. In this study, we analyzed ancient microbial DNA from 483 mammoth remains spanning over 1 million years, including 440 newly sequenced and unpublished samples from a 1.1-million-year-old steppe mammoth. Using metagenomic screening, contaminant filtering, damage pattern analysis, and phylogenetic inference, we identified 310 microbes associated with different mammoth tissues. While most microbes were environmental or post-mortem colonizers, we recovered genomic evidence of six host-associated microbial clades spanning Actinobacillus , Pasteurella , Streptococcus, and Erysipelothrix . Some of these clades contained putative virulence factors, including a Pasteurella -related bacterium that had previously been linked to the deaths of African elephants. Notably, we reconstructed partial genomes of Erysipelothrix from the oldest mammoth sample, representing the oldest authenticated host-associated microbial DNA to date. This work demonstrates the potential of obtaining ancient animal microbiomes, which can inform further paleoecological and evolutionary research.

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organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
aDNA, mammoths, metagenomics, microbes, paleogenetics
in
Cell
volume
188
issue
23
pages
24 - 6619
publisher
Cell Press
external identifiers
  • pmid:40902595
  • scopus:105017056807
ISSN
0092-8674
DOI
10.1016/j.cell.2025.08.003
language
English
LU publication?
yes
additional info
Publisher Copyright: © 2025 The Authors.
id
ce3d5f7f-31e8-4a27-b4d8-f8f1d6904c14
date added to LUP
2025-12-08 15:04:47
date last changed
2025-12-10 11:06:35
@article{ce3d5f7f-31e8-4a27-b4d8-f8f1d6904c14,
  abstract     = {{<p>Ancient genomic studies have extensively explored human-microbial interactions, yet research on non-human animals remains limited. In this study, we analyzed ancient microbial DNA from 483 mammoth remains spanning over 1 million years, including 440 newly sequenced and unpublished samples from a 1.1-million-year-old steppe mammoth. Using metagenomic screening, contaminant filtering, damage pattern analysis, and phylogenetic inference, we identified 310 microbes associated with different mammoth tissues. While most microbes were environmental or post-mortem colonizers, we recovered genomic evidence of six host-associated microbial clades spanning Actinobacillus , Pasteurella , Streptococcus, and Erysipelothrix . Some of these clades contained putative virulence factors, including a Pasteurella -related bacterium that had previously been linked to the deaths of African elephants. Notably, we reconstructed partial genomes of Erysipelothrix from the oldest mammoth sample, representing the oldest authenticated host-associated microbial DNA to date. This work demonstrates the potential of obtaining ancient animal microbiomes, which can inform further paleoecological and evolutionary research.</p>}},
  author       = {{Guinet, Benjamin and Oskolkov, Nikolay and Moreland, Kelsey and Dehasque, Marianne and Chacón-Duque, J. Camilo and Angerbjörn, Anders and Arsuaga, Juan Luis and Danilov, Gleb and Kanellidou, Foteini and Kitchener, Andrew C. and Muller, Héloïse and Plotnikov, Valerii and Protopopov, Albert and Tikhonov, Alexei and Termes, Laura and Zazula, Grant and Mortensen, Peter and Grigorieva, Lena and Richards, Michael and Shapiro, Beth and Lister, Adrian M. and Vartanyan, Sergey and Díez-del-Molino, David and Götherström, Anders and Pečnerová, Patrícia and Nikolskiy, Pavel and Dalén, Love and van der Valk, Tom}},
  issn         = {{0092-8674}},
  keywords     = {{aDNA; mammoths; metagenomics; microbes; paleogenetics}},
  language     = {{eng}},
  month        = {{11}},
  number       = {{23}},
  pages        = {{24--6619}},
  publisher    = {{Cell Press}},
  series       = {{Cell}},
  title        = {{Ancient host-associated microbes obtained from mammoth remains}},
  url          = {{http://dx.doi.org/10.1016/j.cell.2025.08.003}},
  doi          = {{10.1016/j.cell.2025.08.003}},
  volume       = {{188}},
  year         = {{2025}},
}