Oldest microbial DNA ever seen was found in a 1-million-year-old mammoth

A single molar from a steppe mammoth that died about 1.1 million years ago in northeastern Siberia has preserved tiny fragments of bacterial DNA.

The tooth, found near the Adycha River in Russia, lets scientists study microbes that once lived inside a massive Ice Age herbivore.

By sifting through bacterial DNA from mammoth bones and teeth, researchers uncovered microbes that once lived in and on those animals.

The work links an extinct mammal to bacteria that today still affect elephants, livestock, and people.

Unlocking mammoth’s frozen DNA

Every animal carries a microbiome, the full community of bacteria and other microbes that live in and on its body. For extinct species like mammoths, that hidden ecosystem has usually stayed out of reach.

The work was led by Benjamin Guinet, a researcher at the Swedish Museum of Natural History in Stockholm. His research focuses on ancient DNA, genetic material preserved in very old remains.

A recent study examined microbial DNA in 483 mammoth remains from seven sites in Russia and Canada. The team generated new sequence data from 440 of those samples, including the 1.1 million year old Adycha mammoth molar.

To tease out genuine ancient microbes, the scientists first removed mammoth and human DNA from the sequence files.

They then compared the remaining fragments against a huge database of microbial genomes and kept only short, damaged sequences that covered each genome evenly.

Tracing ancient microbes

The researchers used metagenomics, a method that reads all DNA in a sample at once to reveal which organisms are present. This approach showed both environmental microbes and those that likely lived inside the mammoths during life.

After several rounds of quality checks, they identified 310 ancient microbial species from 105 mammoth specimens. Most appear to be environmental bacteria that colonized the remains after death.

Hidden in that larger list were six groups of bacteria that fit the pattern of being host-associated, meaning they normally live on or inside animals. 

The clearest signs of host association came from teeth and tusks, especially the large chewing teeth called molars. These tissues often preserve oral bacteria that once lived on the tooth surface or in the gums.

Microbial lineages in mammoths

One of the most striking finds involves the genus Erysipelothrix, a group of rod shaped bacteria that can infect many animals. 

The team reconstructed partial genomes of an Erysipelothrix strain from the 1.1 million year old steppe mammoth molar, making it the oldest authenticated host-associated microbial DNA recovered so far.

Some relatives of this bacterium have been linked to heart valve infections in dogs, and one veterinary report described Erysipelothrix tonsillarum in several dogs with endocarditis, a dangerous inflammation of the inner lining of the heart.

Those modern cases show that bacteria similar to the mammoth strain can sometimes move from quiet passenger to serious pathogen.

Oral bacterial DNA from mammoths

Another group of mammoth associated microbes belonged to Streptococcus, a diverse genus that includes both harmless residents and disease causing strains. 

In people, Streptococcus mutans is a major cause of dental caries, the medical term for tooth decay, according to one microbiology review, and the mammoth Streptococcus lineages were distantly related to S. mutans and to Streptococcus devriesei, a tooth associated species in horses.

These patterns suggest that mammoths carried their own distinct oral bacteria that sometimes damaged their teeth. The same microbial groups that quietly live in the mouths of modern animals may have been chewing away at mammoth enamel long before humans appeared.

Pasteurella-like bacteria formed two additional clades in the mammoth dataset. In 2020, a Pasteurellaceae strain known as Bisgaard taxon 45 was implicated in fatal septicemia, a serious blood infection, in six African elephants in Zimbabwe.

The mammoth Pasteurella from Late Pleistocene bones were closely related to that elephant strain. The connection raises the possibility that similar bloodstream infections affected at least a few mammoths.

What this says about mammoth health

Not all of the microbes recovered from the mammoths were likely killers. Many bacteria live as commensals, microbes that normally occupy a host without causing disease until conditions change.

One clade of mammoth associated bacteria was most closely related to Basfia succiniciproducens, a rumen bacterium that naturally produces large amounts of succinic acid in the guts of cattle. 

Succinic acid is an important intermediate in energy metabolism, so similar microbes in mammoths may have helped break down tough plant material.

The genomic data also revealed potential virulence, the capacity of a microbe to cause serious disease, in several of the mammoth associated strains. 

Some Pasteurella and Streptococcus lineages carried gene variants linked to toxins, biofilm formation, or surface molecules that help bacteria invade tissues.

For Erysipelothrix, modern relatives can cause septicemia and endocarditis in livestock and wildlife. A veterinary manual notes that Erysipelothrix rhusiopathiae infections in pigs range from sudden bloodstream disease to chronic joint problems.

Taken together, the mammoth microbial genomes hint at a mix of helpful gut partners, neutral passengers, and occasional troublemakers. That balance matches what is seen in modern animals, where most microbes are harmless or beneficial but a few can cause severe illness.

Lessons from ancient mammoth DNA

By capturing snapshots of host associated microbes over more than one million years, this study stretches the timeline of microbiome research far beyond modern animals.

It also shows that fast evolving bacteria can still be traced in deep time when preservation is just right.

The results add a new layer to studies of mammoth evolution based on their own genomes and fossils. Host microbes may have shaped how these Ice Age herbivores digested food, resisted infections, and coped with shifting climates.

The same methods could be applied to other frozen or well preserved remains, from ancient horses to extinct cave bears.

Future work that targets dental calculus, the hardened plaque on teeth, may reveal even richer ancient microbial communities in mammoths and their neighbors.

“This work opens a new chapter in understanding extinct species. We can now look beyond mammoth genomes and explore the microbial communities that lived inside them,” said Love Dalén, Professor of Evolutionary Genomics at the Centre for Palaeogenetics.

The study is published in Cell.

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