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Ancient teeth preserve microbial genomes beyond a million years
An international research team led by the Centre for Palaeogenetics (Stockholm University and the Swedish Museum of Natural History) has recovered microbial DNA from woolly and steppe mammoth remains that dates back more than one million years. Published in Cell, the study represents the oldest host-associated microbial DNA ever identified and provides a rare window into the microbiomes of extinct megafauna.
The team analyzed microbial sequences from 483 mammoth specimens, 440 of which were sequenced for the first time. Among the samples was a steppe mammoth dated to about 1.1 million years ago. Using state-of-the-art ancient DNA extraction, high-throughput sequencing, and rigorous bioinformatic filtering, researchers separated microbes that likely lived in or on living mammoths from those that colonized remains postmortem. The project combined paleogenetics and microbial genomics to push the preservation limits for host-associated DNA far earlier than previously reported.
"Imagine holding a million-year-old mammoth tooth. What if I told you it still carries traces of the ancient microbes that lived together with this mammoth? Our results push the study of microbial DNA back beyond a million years," said Benjamin Guinet, postdoctoral fellow and lead author. "This opens new possibilities to study how host-associated microbes evolved in parallel with their hosts."
Methods, microbial lineages, and reconstructed genomes
The researchers applied targeted metagenomic sequencing and contamination-aware computational pipelines to detect authentic ancient microbial signals. Analyses revealed six microbial clades repeatedly associated with mammoth tissues across time and geography. These include relatives of Actinobacillus, Pasteurella, Streptococcus, and Erysipelothrix—genera known today for host associations ranging from commensalism to disease.
Notably, the team reconstructed partial genomes of Erysipelothrix from the 1.1-million-year-old steppe mammoth, producing the oldest host-associated microbial genomic fragments on record. One Pasteurella-related lineage identified by the study is closely related to a pathogen implicated in fatal outbreaks among African elephants, raising the possibility that similar infections could have affected mammoth populations. However, distinguishing pathogenic impact from background colonization remains challenging due to DNA degradation and limited clinical comparators.
"As microbes evolve fast, obtaining reliable DNA data across more than a million years was like following a trail that kept rewriting itself," said senior author Tom van der Valk. "These finds show that ancient remains can preserve biological insights far beyond the host genome."
Ecological and evolutionary implications
The discovery that certain microbial lineages coexisted with mammoths for hundreds of thousands of years suggests stable host–microbe relationships across Pleistocene ecosystems. These associations spanned large geographic ranges and temporal scales—from over a million years ago until the last woolly mammoths on Wrangel Island roughly 4,000 years ago. While the study cannot definitively prove that microbes drove declines or extinctions, it highlights microbes as an underexplored factor in megafaunal health, adaptation, and resilience.
The research also illustrates how paleogenomics and metagenomics together can reconstruct aspects of extinct species’ biology beyond nuclear or mitochondrial DNA, extending to disease ecology and microbial evolution.
Expert Insight
Dr. Elena Ruiz, a fictional paleomicrobiologist at the University of Cambridge, comments: "Recovering host-associated microbes from million-year-old material is a technical tour de force. These data let us trace ancient disease-related lineages and ask whether long-term host–microbe coevolution influenced megafaunal survival. Future sampling and experimental work will be crucial to link microbial genomes with pathology or immunity in extinct animals."
Conclusion
This study expands the frontier of ancient DNA research by demonstrating that host-associated microbial DNA can persist for over a million years. By sequencing hundreds of mammoth specimens and reconstructing partial microbial genomes, researchers uncovered long-lived bacterial lineages—including candidates related to modern elephant pathogens. The findings provide new tools and questions for paleogenetics, microbial evolution, and the ecology of extinct megafauna, underscoring the role of microbes in the deep history of life on Earth.
Source: sciencedaily
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