Million year-old mammoth microbes reveal new clues about disease

A new study reports microbial DNA preserved inside woolly and steppe mammoth remains that are older than one million years. The team shows that some bacteria were living with these animals while they were alive, not just invading after death.

Researchers analyzed DNA from 483 specimens and sequenced 440 of them for the first time. From a steppe mammoth that lived about 1.1 million years ago, they even pieced together parts of bacterial genomes that once infected or inhabited the animal.

Ancient microbes in mammoths

The work was led by Benjamin Guinet, a postdoctoral fellow at the Centre for Palaeogenetics in Stockholm (CPG). The Centre is a collaboration between Stockholm University and the Swedish Museum of Natural History (NRM).

“Our results push the study of microbial DNA back beyond a million years, opening up new possibilities to explore how host-associated microbes evolved in parallel with their hosts,” said Guinet.

The project involved an international team of experts working across multiple collections and labs.

The researchers used strict lab protocols, computational filters, and DNA damage checks to separate life stage microbes from postmortem contaminants. That approach helped them focus on organisms that were likely part of the mammoth’s own internal community.

Inside mammoth DNA

The scientists kept finding the same six types of bacteria in mammoth remains from different times and places, including close relatives of Actinobacillus, Pasteurella, Streptococcus, and Erysipelothrix.

This pattern suggests that these microbes had a long history with mammoths, sticking with them through environmental changes and population shifts.

The scientists distinguished host-associated microbes, meaning those living in or on a host while it was alive, from environmental bacteria that entered after burial.

They used metagenomics, a method that reads all DNA in a sample at once, then identified ancient damage patterns to authenticate the oldest material.

From the 1.1 million year steppe mammoth, the team reconstructed partial genomes of Erysipelothrix that likely came from an infection during life. This is the oldest authenticated host-associated microbial DNA ever reported, and it extends the range for studying ancient host microbe interactions.

Why ancient microbes matter

This result builds on earlier work that recovered genome scale data from mammoth teeth more than one million years old, demonstrating that DNA can survive when conditions are right.

The previous research established methods and expectations for data quality at this extreme age.

Ancient DNA is fragile and breaks into tiny pieces, and chemical changes accumulate over time. By tracking these signatures, scientists can tell ancient sequences from modern contamination and avoid false signals.

“As microbes evolve fast, obtaining reliable DNA data across more than a million years was like following a trail that kept rewriting itself,” said study senior author Tom van der Valk.

“Our findings show that ancient remains can preserve biological insights far beyond the host genome, offering us perspectives on how microbes influenced adaptation, disease, and extinction in Pleistocene ecosystems.”

The Pleistocene was a period from about 2.6 million years ago to 11,700 years ago that included repeated ice ages.

Microbes linked to mammoth health

One bacterium in the dataset is closely related to a Pasteurella species implicated in lethal outbreaks among African elephants. That connection is supported by a 2023 paper that identified a Pasteurella relative as the likely cause of fatal septicemia in elephants in Zimbabwe.

The new study reports several putative virulence factors, which are gene features tied to disease-causing ability, in some clades. The authors are careful about cause and effect because ancient DNA is incomplete and infections leave mixed traces.

Erysipelothrix is also known to sicken Arctic wildlife today, including muskoxen during unusual mortality events. That pattern has been documented in a Canadian Veterinary Journal that found Erysipelothrix rhusiopathiae associated with widespread deaths in the Canadian Arctic.

Mammoth survival and microbes

Microbes that stayed with mammoths for hundreds of thousands of years hint at stable relationships shaped by diet, climate, and social behavior. The persistence of these lineages across far flung regions points to deep coevolution.

The last woolly mammoths survived on Wrangel Island until about 4,000 years ago, long after mainland populations vanished. Genetic work on that relict group links their late survival to small population size and accumulating harmful mutations.

“This work opens a new chapter in understanding the biology of extinct species. Not only can we study the genomes of mammoths themselves, but we can now begin to explore the microbial communities that lived inside them,” said Love Dalén, professor of evolutionary genomics at the CPG.

Ultimately, the data help connect health, ecology, and extinction risks in a single picture.

Where this research can go next

Reconstructing ancient microbiomes can help set baselines for living elephant microbiomes. That matters because health, diet, and stress are all reflected in the microbiome, the community of microbes that live in and on an organism.

Ancient pathogen signals can also clarify whether outbreaks played a role in population declines. Learning which bacteria carried disease associated genes in the past could inform surveillance and treatment strategies for modern elephants.

Finally, the same tools can be applied to other Ice Age species to test whether long-lived microbial partners were the rule rather than the exception. Careful sampling, clean labs, and independent checks will keep new claims on firm ground.

The study is published in the journal Cell.

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