The bacteria in our mouth are not only important for our health, they also provide valuable information about our evolution. From the plaque of various monkey species as well as Neanderthals and Homo sapiens from the last 100,000 years, researchers reconstructed which bacteria colonized the mouths of our ancestors and distant relatives. Some groups of bacteria have probably been with us for 40 million years. The fossil oral flora also gives astonishing insights into the diet of the earliest humans and also suggests possible pairings between humans and Neanderthals.
Hundreds of different types of bacteria live in our mouths. Many contribute to a healthy environment, others can cause diseases such as tooth decay and periodontal disease. They cavort in our saliva and on our mucous membranes and form a biofilm on our teeth. This biofilm can remain in the form of tartar for thousands of years. In this way, fossil teeth can be used to determine which bacteria once lived on them.
100,000 year old tartar
A team led by James Fellows Yates from the Max Planck Institute for the History of Human History in Jena has now examined the dental plaque of 124 individuals, including people living today, gorillas, chimpanzees and howler monkeys, as well as fossils from early modern humans and Neanderthals. Using new computer-based approaches, the researchers reconstructed the microbiome from the mouths of our ancestors from the DNA in the fossilized tartar and compared it with today’s individuals.
“We were able to show that bacterial DNA from the oral flora can be retained for at least twice as long as previously assumed,” says Yates. The oldest genome studied came from a Neanderthal man from the Pešturina Cave in Serbia and was 100,000 years old – more than 50,000 years older than the previously oldest reconstructed microbiome. “The tools and techniques developed in this study open up new avenues for answering fundamental questions in microbial archeology and will enable broader exploration of the relationship between humans and their microbiome,” said Yates.
Coevolution between bacteria and host
Together with his colleagues, he identified ten groups of bacteria in the plaque that were found in all of the individuals examined. Since these bacteria were even found in the only distantly related howler monkeys, the researchers assume that this core microbiome developed 40 million years ago. “Most of the bacteria that are part of the nuclear microbiome are now known to play important structural and functional roles in the formation and maturation of plaque,” the researchers explain. “This suggests deep coevolutionary relationships between these taxa and their hosts.”
In addition to some health-promoting bacteria, Yates and colleagues also found bacteria that are now associated with the development of periodontal disease. “Their presence in the core microbiome supports the hypothesis that they are not pathogens in the traditional sense, but that their pathogenic character in modern humans could be related to an imbalance between the biofilm and the host,” the researchers said.
Insights into lifestyle and nutrition
Apart from this core microbiome, the researchers found that the oral flora of humans and Neanderthals are particularly similar. In particular, a group of early people from Ice Age Europe shared with the Neanderthals living at the same time some strains of bacteria that were not found in other people then and now. Since the oral microbiome is typically acquired by caregivers in early childhood, the researchers believe that this result suggests that Neanderthals and early humans not only reproduced with each other, but also cared for their children together. “Oral bacteria offer a surprising opportunity to reconstruct the interactions between humans and Neanderthals tens of thousands of years ago,” says Yates colleague Irina Velsko. “The overlap between human and microbial evolutionary biology is fascinating.”
The researchers also made a surprising discovery with regard to the diet of our ancestors: In people then and now, as well as in Neanderthals, they found a subgroup of streptococci that have specially adapted to the consumption of starch – even in individuals who long before lived the introduction of arable farming. This suggests that our ancestors ate starch-rich foods such as tubers, roots and seeds earlier than expected. This high-energy food may even have helped develop the large brain typical of our species.
“Reconstructing what was on the menu for our earliest ancestors is a huge challenge, but our oral bacteria can provide important clues to understanding the early dietary changes that made us unique,” says Yates colleague Christina Warinner. “Bacterial genomes evolve much faster than the human genome, which makes our microbiome a particularly sensitive indicator of important events in our distant and recent evolutionary past.”
Source: James Fellows Yates (Max Planck Institute for the History of Man, Jena) et al., Proceedings of the National Academy of Sciences, doi: 10.1073 / pnas.2021655118