A reconstruction of oral microflora genomes spanning a whopping 100,000-year period of human history may have revealed a surprising shift in the types of bacteria that like to call our mouths home.
Researchers from across Germany and the US teamed up to decode DNA extracted from dental plaque from human and Neanderthal remains, using the sequences to recreate proteins once used by bacteria.
It’s a big moment in the study of microbes that humans harbor, giving us insight into bacteria that are no longer part of our body’s personal ecosystem. In the future, these findings could even be used to develop new drug treatments.
Tartar, or calcified dental plaque, is a perfect hiding place for microbes, which is why your dentist stresses the importance of brushing and flossing daily. As good as it is at protecting bacteria, the researchers were only able to extract very small fragments of DNA from the old samples to work with. That left a lot of scientific detective work to decipher the sequences.
“A typical bacterial genome is 3 million base pairs long, but time fragments the ancient DNA we recover to an average length of only 30 to 50 base pairs,” says anthropologist Christina Warinner of Harvard University in Massachusetts.
“In other words, each ancient bacterial genome is like a 60,000-piece puzzle, and each piece of dental tartar contains millions of genomes.”
The researchers started with plates from 12 Neanderthals (between 40,000 and 102,000 years old) and 34 humans (between 150 and 30,000 years old).
Previously, such genetic snippets would have been compared to the genomes of modern microbial species, a useful reference, but one that will never reveal new or extinct species.
In this case, the researchers refined a process known as the de novo assembly technique, where smaller fragments of DNA can be built to form a complete genome.
It’s a bit like trying to put together a puzzle with just a few of the pieces and no picture to work from. A variety of tricks, including identifying overlaps and patterns, are implemented to try to fill in the gaps, and after three years of careful comparison and analysis on all samples, the bacterial genomes could be reconstructed.
From the high-quality genomes, the researchers identified a shared sequence called biosynthetic gene clusters. Genes within these groups play important roles in building proteins within bacteria.
“This is how bacteria make really complicated and useful chemicals.” says Warinner. “Almost all of our antimicrobials and many of our drug treatments are ultimately derived from such bacterial biosynthetic gene pools.”
By transferring reconstructed DNA sequences into modern bacteria, the researchers successfully produced enzymes based on the ancient blueprints of microbes that once lived inside our ancestors’ mouths. One of these enzymes produced organic molecules known as furans, which today are involved in signaling between bacterial cells.
Based on a study of the genes on either side of the furan-producing enzyme, the researchers suspect that this particular version might play a role in regulating bacterial photosynthesis.
In all, the largest number of high-quality sequences appeared to belong to a genus of bacteria called chlorobium. Capable of using light to oxidize sulfur for energy, these microbes aren’t exactly the kind of organisms we’d expect to be nestled against our teeth.
It is possible that they once lived in the human mouth, absorbing the few rays that warmed our tonsils every time we opened our mouths. Or they were a consequence of drinking water from the pond.
While we’re not talking about bringing microbes back to life here, a bacterial version of Jurassic Park – ancient genomes are useful in telling scientists how our microbiome might have changed and evolved over tens of thousands of years.
For example, there is the question of why these bacteria are no longer in our mouths, perhaps due to a change in behavior or drinking habits, which is something that could be explored in future research.
“Now we can scale up this process,” says Warinner. “Suddenly, we can vastly expand our understanding of the biochemical past.”
The research has been published in Science.
