100,000 year-old Neanderthal oral microbiomes reveal evolutionary clues

Scientists have analyzed the fossilized dental plaque of Neanderthals to sequence the oral microbiome, including the oldest ever, at 100,000 years old. By comparing them to humans and other primates, the study reveals new insights into how this symbiotic human-microbe relationship evolved – and might even have contributed to the growth of our brains.

Communities comprising trillions of microbes live on and in our bodies – but before you break out the hand sanitizer and mouthwash, remember that these microbiomes are crucial to our health. They play a role in processes like digestion, and can influence our likelihood of developing various diseases.

But despite our microbiome being such an integral player in our overall health, not much is known about how it evolved alongside us. So for the new study, an international team of scientists set out to piece together this history.

“For a long time, people have been trying to understand what a normal healthy microbiome is,” says Harvard Professor Christina Warinner, an author of the study. “If we only have people today that we’re analyzing from completely industrialized contexts and that already have high disease burdens, is that healthy and normal? We started to ask: What are the core members of the microbiome? Which species and groups of bacteria have actually co-evolved with us the longest?”

Rings of hardened dental plaque can be seen around the middle of these teeth, from a wild chimpanzee’s jawbone

Richard Wrangham

A previous study sought to answer the question by looking at 50,000-year old Neanderthal poop, but for the new work researchers looked to the other end. The team studied the oral microbiomes of 124 individuals, including the fossil remains of Neanderthals and humans dating back as far as 100,000 years, and present-day humans, chimpanzees, gorillas and howler monkeys.

The researchers identified 10 strains of bacteria that were common to all of the tested species at all ages, implying they’ve been an integral part of the shared hominid oral microbiome since before our last common ancestor, around 40 million years ago.

The team also found that the oral microbiomes of Neanderthals and present-day humans are surprisingly similar. Of the few differences, certain bacteria seemed to have disappeared from the human microbiome around 14,000 years ago.

But perhaps the most important find was the strains of Streptococcus shared by Neanderthals and humans (both present and ancient), but not the other primates. These bacteria are known to feed on starch, hijacking enzymes from our own saliva to break it down.

The implications of this could be massive. For these bugs to be there, Neanderthals and ancient humans had to have been eating starchy foods, suggesting they became important even before the advent of agriculture. The high glucose content could even have helped fuel the rapid growth of our brains.

“We think we’re seeing evidence of a really ancient behavior that might have been part of encephalization — or the growth of the human brain,” says Warinner. “It’s evidence of a new food source that early humans were able to tap into in the form of roots, starchy vegetables, and seeds.”

The comprehensive study helps put our microbiomes into new contexts, and the researchers say it gives new clues to the evolution of both ourselves and our microbial buddies.

The study was published in the journal PNAS.

Sources: Harvard Gazette, PNAS

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