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Guinet B, Oskolkov N, Moreland K, Dehasque M, Chacón-Duque JC, Angerbjörn A, Arsuaga JL, Danilov G, Kanellidou F, Kitchener AC, Muller H, Plotnikov V, Protopopov A, Tikhonov A, Termes L, Zazula G, Mortensen P, Grigorieva L, Richards M, Shapiro B, Lister AM, Vartanyan S, Díez-Del-Molino D, Götherström A, Pečnerová P, Nikolskiy P, Dalén L, van der Valk T
Cell - (-) - [2025-09-02; online 2025-09-02]
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ancient microbial DNA from 483 mammoth remains spanning over 1 million years, including 440 newly sequenced and unpublished samples from a 1.1-million-year-old steppe mammoth.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.
NGI Stockholm (Genomics Production) [Service]
National Genomics Infrastructure [Service]
PubMed 40902595
DOI 10.1016/j.cell.2025.08.003
Crossref 10.1016/j.cell.2025.08.003
pii: S0092-8674(25)00917-1