Ancient bacteria reveals the critical food early humans ate

The gut is the darling of human microbiome research. But with over 700 species of bacteria, the human mouth hosts the second largest and most diverse microbiome in the body.

According to new research, understanding ancient oral microbe communities can help modern-day scientists better understand major events in human evolution and even treat health conditions in the future.

“The microbes that live on your body are just as important to your body as an organ like your liver or heart, so making sure we keep these microbes happy and healthy is just as important. But to do that, we really need to understand how they work,” James Fellows Yates tells Inverse.

Fellows Yates is a biomolecular archaeology Ph.D. student at the Max Planck Institute for the Science of Human History and co-author of a paper published Monday in the journal Proceedings of the National Academy of Sciences examining the evolution of the oral microbiome.

Most of what we understand about the oral microbiome has come from samples taken from industrialized societies that have incorporated mouthwash and floss into daily life. Far less is known about the global diversity of oral microbes in unindustrialized and ancient humans.

This is important because the oral microbiome is often implicated in mouth diseases. Research like this new study suggests the presence or absence of certain microbes likely aren’t to blame. Instead, it may be driven by an imbalance in the microbial ecosystem.

“There is a lot we don’t know about these microbial communities and we need to explore them in a lot of different species, including ourselves, to get an understanding of that microbial diversity,” Fellows Yates tells Inverse.

What to know first — All microbiomes include a core microbe, which is more or less the same in all members of a species, and a variable microbiome, which varies between individuals based on what they eat, where they live, and physiological differences.

Fellows Yates and colleagues discovered that a set of core oral microbes have remained consistent throughout African hominid evolution, and are shared today by modern humans, gorillas, and howler monkeys.

Like the microbes living in the human gut, scientists are just beginning to understand how each of these oral microbe species evolved to live here and what they mean for the health of modern-day humans.

Examining the bacteria living in dental tartar — plaque that mineralizes onto teeth — is also a reliable way to collect clues about ancient life. Teeth don’t break down like soft organs do, so fossilized microbes stay preserved for millennia. The gut microbiome is also extremely susceptible to change, whether that be from antibiotics, diet, lifestyle, or external factors.

Plaque is the opposite. The oral microbiomes that live in tooth build-up are typically quite stable, especially among all the species in a genus.

What’s new — Fellows Yates and his team made two important findings.

First, a group of modern and ancient primates that includes gorillas, Neanderthals, and humans appears to have the same core oral microbe. The team identified 10 core bacterial genera that have remained consistent throughout African hominid evolution, which are also found in howler monkeys.

“These starch and sugar-rich diets allowed hominids to have a bigger brain and evolve as we have.”

This preservation suggests that this specific microbial make-up may have played an important role in health for more than 40 million years, Fellows Yates explains.

But the human core biome was different in one key way. Compared with non-human hominids, humans uniquely have an abundance of Streptococcus species, which are responsible for converting starches to sugars.

“These starch and sugar-rich diets allowed hominids to have a bigger brain and evolve as we have,” Fellows Yates says. The human brain, for its part, uses up to one-quarter of the body's energy and as much as 60 percent of blood glucose. The team views this finding as evidence of an ancient behavior that led to this bigger brain.

How they did it — The team identified and analyzed 89 dental plaque samples from different primates, including Neanderthals, howler monkeys, chimpanzees, and modern-day humans. To do this, they used the largest database of sequenced human diversity as a reference and compared the ancient DNA to known samples. That’s how they were able to match the broken pieces of ancient microbial DNA to the full strands needed for identification.

This revealed the 10 bacterial genera that have remained consistent deep into human history and that may hold important information about modern-day human health.

When it comes to better understanding what ancient hominid diets consisted of, and when they changed, preserved tartar holds a record of plants that have long disappeared. The team found that humans who lived in the Pleistocene Epoch, which ended about 11,700 years ago, ate diets that varied as much as modern humans’ diets do today — although this variation would look different spread across a dinner table. Around this time, ancient humans all ate a mix of starchy tubers (tubers are starchy options like yams and potatoes), fruits, and rhizomes.

Meanwhile, dental plaque sourced from ancient humans living in South Africa revealed they ate starchy grass seeds as far back as 170,000 years ago — this was also found in samples from Skhul, Israel that date to about 120,000 years ago. This study suggests an adaptation for eating starch-rich foods began earlier than previously thought.

Why it matters — This study suggests previous attempts to understand how the oral microbiome influences diseases have been limited by population samples taken only from people living in modern, industrialized societies.

“We need to understand how the microbial communities might be different in different microbiomes and groups of people.”

According to Fellows Yates, this research method — comparing bits of ancient DNA to sequences of known DNA housed in a database of samples mostly taken from industrialized countries — was just an initial step toward course correcting.

“This reference-based approach is a big thing at the moment and we know we need to get away from that,” he says. But that’s easier said than done since the methods used to reconstruct modern DNA can’t be used for ancient DNA.

Working only with a database that focuses on samples taken from the Western world creates bias and doesn’t allow palaeogeneticists to identify currently unknown ancient microbes, Fellows Yates explains. And if palaeogeneticists can figure out a way to identify ancient microbes without requiring a reference, they might be able to identify extinct microbes.

In regard to oral health, modern oral hygiene practices might be hiding the root causes of disease. Moving away from the Western-focused model will allow health treatments to be more equitable among all people, regardless of where they live.

“We know that the microbiome plays a huge role in health, and if we want to make sure that healthcare treatments are designed to help everyone, we need to understand how the microbial communities might be different in different microbiomes and groups of people,” Fellows Yates says.

“Moving away from this reference model will allow us to do that.”

Abstract: The oral microbiome plays key roles in human biology, health, and disease, but little is known about the global diversity, variation, or evolution of this microbial community. To better understand the evolution and changing ecology of the human oral microbiome, we analyzed 124 dental biofilm metagenomes from humans, including Neanderthals and Late Pleistocene to present-day modern humans, chimpanzees, and gorillas, as well as New World howler monkeys for comparison. We find that a core microbiome of primarily biofilm structural taxa has been maintained throughout African hominid evolution, and these microbial groups are also shared with howler monkeys, suggesting that they have been important oral members since before the catarrhine–platyrrhine split ca. 40 Mya. However, community structure and individual microbial phylogenies do not closely reflect host relationships, and the dental biofilms of Homo and chimpanzees are distinguished by major taxonomic and functional differences. Reconstructing oral metagenomes from up to 100 thousand years ago, we show that the microbial profiles of both Neanderthals and modern humans are highly similar, sharing functional adaptations in nutrient metabolism. These include an apparent Homo-specific acquisition of salivary amylase-binding capability by oral streptococci, suggesting microbial coadaptation with host diet. We additionally find evidence of shared genetic diversity in the oral bacteria of Neanderthal and Upper Paleolithic modern humans that is not observed in later modern human populations. Differences in the oral microbiomes of African hominids provide insights into human evolution, the ancestral state of the human microbiome, and a temporal framework for understanding microbial health and disease.