Scientists Sequence Bacterial DNA from Germs in Mammoth Teeth

A Mammoth Toothache: Bacterial Community Discovered in Mouth of Ancient Mammoth

By Katie Kavanagh & Nature magazine

An analysis of the bones and teeth of ancient mammoths (Mammuthus) has identified some of the microorganisms that lived in the animals’ mouths and bodies more than one million years ago.

The study, published in Cell on 2 September, describes the oldest microbial DNA ever sequenced, and reveals that some species of pathogenic bacteria that have been linked to the deaths of African elephants (Loxodonta africana) once infected the mouths of their ancient cousins.

The findings offer “a good opportunity to get a global picture about what kind of bacteria or viruses we could find in this extinct species”, says study co-author Benjamin Guinet, a palaeomicrobiologist at the Centre for Palaeogenetics in Stockholm, Sweden. Further research could provide insights into how microbes might have helped ancient animals to adapt to varied environments, and whether they might have been involved in the extinction of these species.

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Pathogenic microbes

Previous research on ancient remains has focused mainly on the DNA of humans and human-associated microorganisms, and few studies have looked at microbe–host interactions in prehistoric animals.

To investigate the relationship between mammoths and microorganisms, the researchers analysed ancient microbial DNA from samples of teeth, skulls and skin from 483 mammoths. The specimens encompass a range of geographical locations, from North America and Britain to Siberia, and date from the Early Pleistocene — around one million years ago — to the extinction of the last mammoths on Wrangel Island (a remote island off the coast of Siberia) during the Holocene, 4,000 years ago.

The researchers identified 310 microbial species that were associated with the mammoth tissues. Many of these were environmental microorganisms that would have colonized the tissues after death, so the team first filtered out the DNA sequences of these post-mortem bacteria. This allowed them to focus on the bacteria that lived inside the mammoths when they were alive.

Using metagenomic screening — a technique for sequencing genetic material in samples that contain genomes from a mixture of organisms — the researchers analysed the DNA present in the mammoth specimens. They then used phylogenetic inference to identify the bacterial genera, by comparing the ancient microbial sequences with those of modern bacteria.

The analysis found six microbial groups associated with the hosts, some of which might have caused diseases in the mammoths. These included a strain similar to Actinobacillus, which has previously been isolated from pig (Sus domesticus) faeces and is thought to be part of the mammoth oral microbiome. They also identified Pasteurella, a bacterial genus closely related to a pathogen that has been linked to the deaths of several African elephants in Botswana and Zimbabwe in 2020. The pathogen infected the mouths of the elephants, then made its way to the bloodstream, causing fatal septicaemia.

The team also reconstructed genomes of a family of bacteria called Erysipelothrix from samples from four woolly mammoths and from a 1.1-million-year-old steppe mammoth, which is the oldest host-associated microbial DNA yet discovered. Unlike the other bacterial groups, which were associated only with teeth cells, this microorganism was, in the case of the woolly mammal specimens, found in bone tissue.

Ancient microbiomes

The exact effects that these bacterial colonies had on the health of mammoths is difficult to elucidate from this genetic analysis, but the researchers say their study provides a first look at the microbes of ancient animals.

Eva-Maria Geigl, a palaeogeneticist at the Institut Jacques Monod in Paris, questions the biological relevance of analysing samples from more than one million years ago, with a lack of suitable references for comparison. However, she says the team “certainly did good work and produced a lot of data”.

“The paper provides a good proof of concept: even some of the very ancient bacteria can be retrieved genetically,” she adds.

These findings provide a foundation for further research to understand ancient microbiomes and their impacts on health and disease, say the authors.

“It’s just really nice to have this kind of storytelling. We want to open the book of life and push the edges of what we could know,” says Guinet.

This article is reproduced with permission and was first published on September 2, 2025.

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