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 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ancient microbial DNA from 483 mammoth remains spanning over 1 million years, including 440 newly sequenced and unpublished samples from a 1.1-million-year-old steppe mammoth.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.
Authors
- А. В. Протопопов (ORCID: https://orcid.org/0000-0001-6543-4596)
- Michael P. Richards (ORCID: https://orcid.org/0000-0001-5274-8887)
- Grant D. Zazula (ORCID: https://orcid.org/0000-0001-8436-1783)
- Adrian M. Lister (ORCID: https://orcid.org/0000-0002-7985-138X)
- Andrew C. Kitchener (ORCID: https://orcid.org/0000-0003-2594-0827)
- Anders Götherström (ORCID: https://orcid.org/0000-0001-8579-1304)
- Alexei Tikhonov (ORCID: https://orcid.org/0000-0002-7227-5797)
- Marianne Dehasque (ORCID: https://orcid.org/0000-0002-4640-8306)
- Tom van der Valk (ORCID: https://orcid.org/0000-0001-6582-3452)
- Kelsey Moreland (ORCID: https://orcid.org/0000-0002-3571-0876)
- Love Dalén (ORCID: https://orcid.org/0000-0001-8270-7613)
- Gleb K. Danilov (ORCID: https://orcid.org/0000-0002-7125-824X)
- Beth Shapiro (ORCID: https://orcid.org/0000-0002-2733-7776)
- Laura Termes (ORCID: https://orcid.org/0000-0001-6807-1890)
- Héloïse Muller (ORCID: https://orcid.org/0000-0001-5813-4229)
- David Díez‐del‐Molino (ORCID: https://orcid.org/0000-0002-9701-5940)
- Sergey Vartanyan
- Patrícia Pečnerová (ORCID: https://orcid.org/0000-0001-9350-1987)
- Juan Luís Arsuaga (ORCID: https://orcid.org/0000-0001-5361-2295)
- Nikolay Oskolkov (ORCID: https://orcid.org/0000-0001-5326-8893)
- Valerii Plotnikov
- Peter Mortensen
- Foteini Kanellidou
- Benjamin Guinet (ORCID: https://orcid.org/0000-0002-9922-2118)
- Anders Angerbjörn (ORCID: https://orcid.org/0000-0001-5535-9086)
- Pavel A. Nikolskiy (ORCID: https://orcid.org/0000-0001-6547-9890)
- J. Camilo Chacón‐Duque
- L. V. Grigorieva
Institutions
- Université Claude Bernard Lyon 1 (FR)
- École Normale Supérieure de Lyon (FR)
- Universidad Complutense de Madrid (ES)
- Russian Academy of Sciences (RU)
- North-Eastern Federal University (RU)
- Natural History Museum (GB)
- National Museums Scotland (GB)
- Howard Hughes Medical Institute (US)
- Stockholm University (SE)
- Simon Fraser University (CA)
- University of California, Santa Cruz (US)
- Lund University (SE)
- Science for Life Laboratory (SE)
- Swedish Museum of Natural History (SE)
- Government of Canada (CA)
- Academy of Sciences of the Republic of Sakha (RU)
- Peter the Great's Museum of Anthropology and Ethnography (RU)
- Canadian Museum of Nature (CA)
- Geological Institute (RU)
- Centre for Palaeogenetics (SE)
Publication Details
- Journal
- Cell
- Published
- 2025-09-02
- DOI
- https://doi.org/10.1016/j.cell.2025.08.003
- Citations
- 2
- Primary Topic
- Microbial infections and disease research
- Type
- article
- Field-Weighted Citation Impact
- 2.37
Funders
- Knut och Alice Wallenbergs Stiftelse
- Vetenskapsrådet
- European Research Council