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Ancient microbes preserved in mammoth remains
An international team led by the Centre for Palaeogenetics has retrieved microbial DNA from woolly and steppe mammoth remains that dates back more than one million years. The work—reported in Cell—represents some of the oldest host-associated microbial DNA ever recovered and opens a new window onto the long-term interactions between Pleistocene megafauna and their microbial communities. The researchers screened 483 mammoth specimens, including 440 that had not previously been sequenced, and applied advanced genomic and bioinformatic tools to separate microbes that lived with the mammoths from those that colonized their remains after death.
Methods: authenticating microbial signals from deep time
The team combined high-throughput sequencing, damage-pattern analysis and careful contamination controls to distinguish ancient, host-associated microbes from modern environmental contaminants. Samples included teeth, tusks and bone fragments from multiple geographic regions and time periods, with one particularly notable specimen coming from a steppe mammoth dated to roughly 1.1 million years ago. Laboratory work followed strict ancient DNA protocols: dedicated clean-room facilities, negative controls, and bioinformatic filters that identify the characteristic fragmentation and cytosine-to-thymine substitution patterns indicative of degraded ancient DNA.
Bioinformatic approaches also helped partition DNA sequences into groups likely originating from the living microbiome of each animal versus those that arrived after burial. That distinction relies on consistent taxonomic patterns across individuals, preservation signatures, and comparisons with modern relatives. By combining these lines of evidence, the researchers were able to reconstruct partial microbial genomes and establish that some lineages persisted with mammoths across hundreds of thousands of years.
Key discoveries: persistent microbial lineages and potential pathogens
Across the dataset the authors identified six microbial clades repeatedly associated with mammoth remains. These include relatives of Actinobacillus, Pasteurella, Streptococcus and Erysipelothrix—genera known today to include both harmless commensals and pathogenic strains. One Pasteurella-like bacterium found in the study is closely related to a pathogen that has caused lethal outbreaks in modern African elephants, raising the possibility that mammoths shared susceptibility to similar infections.
In a landmark achievement, researchers reconstructed portions of an Erysipelothrix genome from the ~1.1-million-year-old steppe mammoth. This constitutes the oldest authenticated host-associated microbial DNA recovered to date and demonstrates that under favorable conditions, microbial genomes can survive far beyond the host genome's preservation window. The finding expands the temporal scope for studying ancient host-microbe relationships and ancient pathogenic ecology.
Scientific context and implications
Host-associated microbes evolve rapidly relative to their large multicellular hosts; therefore, recovering their genomes from deep time offers a way to study microbial evolution and host-pathogen dynamics over evolutionary timescales. These results suggest that certain microbial lineages coexisted with mammoths across wide geographic ranges and long durations, spanning from more than a million years ago to the late survival of woolly mammoths on Wrangel Island roughly 4,000 years ago.
Tom van der Valk, senior author of the study, emphasizes that ancient remains can preserve biological information beyond the host genome and that these microbial records provide new perspectives on how microbes influenced adaptation, disease and extinction in Pleistocene ecosystems. At the same time, authors caution that DNA degradation, decay-driven bias and limited comparative databases make it difficult to determine the exact impact of these microbes on mammoth health with complete confidence.
Limitations and cautions
Ancient microbial DNA studies face unique challenges: microbial DNA is shorter and more prone to contamination than vertebrate DNA, modern relatives are often poorly represented in reference databases, and taphonomic processes can introduce environmental species into fossil material. The researchers combine multiple authentication criteria to mitigate these issues, but further work—particularly expanding reference genomes for wildlife microbes—will strengthen interpretations.
Technologies and future prospects
Advances in sequencing technology, metagenomic assembly and machine-learning classification have been crucial to this study. As reference databases for microbial genomes grow and computational methods improve, paleomicrobiology will be better able to reconstruct ancient microbial communities, estimate evolutionary rates, and identify genes associated with virulence or host specificity. Ethical and practical considerations will accompany any attempt to synthesize or functionally characterize ancient microbes; the primary value of these findings lies in understanding evolution, ecology and disease dynamics rather than de-extinction.
Applications beyond paleontology
Reconstructing ancient microbes informs modern conservation biology by clarifying historical baselines for host-associated microbiomes and shedding light on pathogen evolution in close relatives of extinct species, such as African and Asian elephants. Insights into past host-pathogen interactions can help veterinary and wildlife health specialists assess long-term disease dynamics and potential risks to endangered species.
Expert Insight
Dr. Elena Rossi, a fictional evolutionary microbiologist at the Institute for Ancient Genomics, comments: "Recovering microbial DNA that is over a million years old is a technical and conceptual milestone. It changes the questions we can ask about co-evolution—moving from snapshots to time series that reveal how microbial communities changed as hosts adapted to shifting climates and landscapes. This work also highlights the need for richer microbial reference databases to interpret ancient signals more precisely."
Future directions
Next steps will include targeted enrichment of candidate pathogen genomes, broader geographic sampling of megafauna remains, and comparative studies with living elephants and other proboscideans. Researchers will also pursue improved methods to authenticate and assemble degraded microbial genomes, and to link specific microbial genes to traits such as antibiotic resistance or virulence. Interdisciplinary collaborations—combining paleogenomics, microbiology, ecology and veterinary science—will be essential to realize the full potential of deep-time microbiome research.
Conclusion
The recovery of microbial DNA from mammoth remains more than a million years old demonstrates that fossil materials can preserve traces of the microbes that lived with extinct animals. Identification of persistent microbial clades—including potential pathogens—provides a unique window into host-microbe co-evolution during the Pleistocene and suggests new avenues for studying disease, adaptation and extinction. While technical and interpretive challenges remain, this study marks a major advance for paleomicrobiology and enlarges our understanding of how microbes have shaped the history of life on Earth.
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