A study published in Cell on September 2nd reported the recovery of the oldest host‑associated microbial DNA ever sequenced from mammoth remains, pushing the study of microbial DNA beyond a million years and revealing hundreds of microbes tied to different mammoth tissues.
The international team analyzed 483 mammoth specimens, 440 of them sequenced for the first time, reconstructed partial genomes of Erysipelothrix bacteria from a 1.1‑million‑year‑old steppe mammoth and four woolly mammoths, and identified six clades that stood out as true host‑associated bacteria, including relatives of Actinobacillus, Pasteurella, Streptococcus, and Erysipelothrix.
“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 Centre for Palaeogenetics.
The analysis also reported that researchers isolated DNA from bacteria that lived inside the mammoths from their teeth and other tissues, tallying 310 microbes associated with different tissues, EL PAÍS reported.
The oldest specimen included a steppe mammoth tooth dated to about 1.1 million years ago from Adycha in the Arctic of present‑day Russia, where permafrost preserves organic remains. The steppe mammoth - Mammuthus trogontherii - an ancestor of the woolly and Columbian mammoths, roamed Northern Eurasia and later North America during the Ice Age.
Using genomics and bioinformatics, the team screened DNA from teeth, skulls, skin, tusks, and bones to distinguish environmental colonizers from microbes that likely lived in mammoths during life. “It’s like searching for a needle in a haystack. The needle is the microbes truly associated with the mammoth, and the haystack is composed of environmental DNA, the mammoth’s own DNA, and laboratory contamination. To find this needle, we relied on careful bioinformatics filtering,” said Benjamin Guinet, a palaeomicrobiologist at the Centre for Palaeogenetics in Stockholm, Sweden, according to El Mundo.
Assisted by a news-analysis system.
Among the findings, a bacterium related to Pasteurella was closely related to a pathogen that caused deadly outbreaks in African elephants. The authors noted that African and Asian elephants are the closest living relatives of mammoths, raising the possibility that mammoths faced similar infections.
The team cautioned that the exact effects of these bacterial colonies on mammoth health were difficult to determine from genetic data alone. Erysipelothrix bacteria can enter the bloodstream and cause infections such as endocarditis and are found in the mouths of pigs and dogs, but whether similar infections occurred in mammoths remained uncertain.
“As microbes evolve fast, obtaining reliable DNA data across more than a million years was like following a trail that kept rewriting itself,” said Tom van der Valk, a researcher at the Centre for Palaeogenetics. The results suggested that some microbial lineages coexisted with mammoths over hundreds of thousands of years, spanning broad geographic areas and evolutionary time scales, from more than a million years ago to the disappearance of woolly mammoths on Wrangel Island about 4,000 years ago.
“We’ve been sequencing mammoths for more than 10 years,” said David Díez del Molino, a researcher at the Centre for Palaeogenetics at Stockholm University. “This work is important because it shows how far we can go with ancient DNA; even to better understand the interactions between microbes and large extinct mammals, and to study how the microbiota may have influenced their adaptation or decline,” said Nicolás Rascován, an Argentine geneticist and researcher at the Pasteur Institute in Paris.