Bacteria have lived on our planet Earth for about 3 billion years, most of the 4.5 billion years the planet has existed. And while hardworking microbes are central to medicine, disease and most areas of the natural worldwe understand little of the form they took in the ancient world.
Stone Age bacteria
now, a new study by an interdisciplinary team made important steps toward understanding Stone Age bacteria by sequencing genomes recovered from ancient dental calculus. The hardened tartar preserved bacterial fragments on the teeth of 12 Neanderthals and 34 humans who lived between 102,000 and 150 years ago. Created by plaque, this tartar fossilized during the lifetime of these individuals, trapping genetic fragments within.
“We have reached an important milestone in uncovering the enormous genetic and chemical diversity of our microbial past,” said one of the authors, Christina Warriner, an associate professor of anthropology at Harvard University. in a press release.
Assembling DNA from the Stone Age
Researchers have puzzled over how to reassemble the ancient DNA fragments into whole or partial genomes, since standard methods of comparing the pieces to today’s databases are not applicable in this case.
The ancient genes were too old and alien, even for the most modern methods designed to connect disparate genetic material. “We had to completely rethink our approach,” said Alexander Hübner, a postdoctoral researcher at the Max Planck Institute for Evolutionary Anthropology, in a press release.
After three years of experimentation, they were able to splice together segments of ancient bacterial DNA about 100,000 base pairs long, enough to begin studying what these microbes were. The team identified many as oral bacteria and others as “exotic species whose genomes have not been described before,” according to the release.
One of them, an unknown species belonging to the genus Chlorobius, contains mysterious genes of unknown function. Modern chlorobia bacteria carry out photosynthesis and can be found in mud and standing water.
A source of new antibiotics?
“After discovering these enigmatic ancient genes, we wanted to take them into the lab to find out what they do,” said Anan Ibrahim, a postdoctoral researcher at the Leibniz Institute for Natural Product Research and Infection Biology, in a press release.
Bacteria produce many chemicals, including drugs, and so researchers wondered what the ancient DNA might code for. Using advanced techniques, they implanted it into modern microbes, which then produced an entirely new biological product, now called “paleofurans.”
The team hopes to eventually find new antibiotics based on Stone Age DNA that could help in combating antimicrobial resistance.
“This is the first step towards accessing the hidden chemical diversity of microbes from Earth’s past and adds an exciting new temporal dimension to natural product discovery,” says Martin Klapper, a postdoctoral researcher at the Leibniz Institute for Natural Product Research and Infection Biology, in press release.