Oldest DNA from poop contains a Neanderthal’s microbiome
February 8, 2021
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El Salt is an open-air rock shelter nestled against the base of a limestone cliff. Archaeological evidence tells us that Neanderthals lived here from around 60,700 to 45,200 years ago.
Enlarge / El Salt is an open-air rock shelter nestled against the base of a limestone cliff. Archaeological evidence tells us that Neanderthals lived here from around 60,700 to 45,200 years ago.

Candela et al. 2021

Biologist Marco Candela and his colleagues recently sequenced ancient microbial DNA from 50,000-year-old Neanderthal feces found at the El Salt archaeological site in Spain. The sequences included DNA from several of the microbes that still call our intestines home, as well as a few that have nearly vanished from today’s urban dwellers. According to Candela and his colleagues, their results suggest that the microscopic population of our guts may have been with us since at least 500,000 years ago, in the era of our species’ last common ancestor with Neanderthals.

Digging up Neanderthal poop

Mixed in with the layer of sediment that once formed the floor of a Neanderthal rock shelter in eastern Spain, archaeologists found millimeter-sized coprolites (fossil poop) and chemical signatures of human feces. An earlier study, published in 2014, sifted through the tiny coprolites to look for traces of Neanderthal diets. “These samples therefore represent, to our knowledge, the oldest known positive identification of human fecal matter,” wrote Candela and his colleagues.

They recently returned to El Salt for new samples, which they scoured for fragments of ancient DNA from the bacteria and other microbes that once lived in the intestines of Neanderthals. To weed out possible contamination, Candela and his colleagues sorted out the old, obviously degraded ancient DNA from the more pristine modern sequences. Most of the ancient DNA in the sediments came from bacteria that lived in the soil and water—tiny relics of the Pleistocene environment. But the rest included some familiar companions.

“There are probably more differences between the gut microbiomes from modern traditional (rural, hunter gatherers) populations and the modern industrial urban populations than between Neanderthal and modern traditional populations,” Candela, a biologist at the University of Bologna, told Ars.

What lived in a Neanderthal’s colon?

Humans and our closest living relatives, chimpanzees, share microbes from the same 24 phylogenetic families. To distinguish the gut microbiome of a human from that of a chimpanzee, you have to look at the genera, species, and sometimes even strains of the micro-organisms from each family. Each species of ape has a distinctive ecosystem of microbes, adapted to live with its immune system and the particular environment of its digestive tract that result from diet.

But some of the key players in modern gut microbiomes—the same genera and species swimming around in your intestines right now, modulating your immune system and breaking down your fiber intake—also lived inside Neanderthals.

In the 50,000-year-old feces-laden sediments from El Salt, Candela and his colleagues identified several key members of the human gut microbiome, like the aptly named Faecalibacterium and the somewhat ironically named Roseburia, both of which help break down dietary fiber into shorter chemicals that your body can metabolize. The team also found the genus Bifidobacterium, which helps digest sugars in milk and also plays a key role in the early childhood immune system. It’s “one of the human commensal bacteria of greatest current interest, due to its very promising potential as a biomarker of a healthy gut microbiome,” they wrote.

According to Candela and his colleagues, the findings suggest that some of the most important members of our gastrointestinal menagerie—the “keystone taxa,” as Candela and his colleagues put it—have been with us even longer than modern humans have existed. If our species and Neanderthals share a common core cast of gut microbes, it suggests that those keystone taxa probably lived in the guts of the last common ancestor both species shared.

Meet some really old friends

Some of those microbes, like the bacterial genus Bifidobacterium, seem to get passed down from mother to child. Others are acquired from the environment or from close contact with others. Those things don’t happen as much in modern urban settings (and that was true before the COVID-19 pandemic). Scientists who study the human microbiome have noticed that, for several generations, certain microbes have been disappearing from the intestines of urban populations in places like the US and Europe. That is mostly thanks to the use of certain medications and disinfectants; a sparkling clean house is, it turns out, a double-edged sword.

The disappearing bacteria include genera in the family Spirochaetaceae, along with the genera Prevotella and Sesulfovibrio. Microbiome researchers call them “old friends,” and their presence in the long-buried Neanderthal feces at El Salt suggests that these microbes are very old friends indeed.

And that’s what Candela meant when he told Ars that modern hunter-gatherers’ gut microbiomes have more in common with Neanderthals than with modern people in industrialized cities. Our gut microbes have changed more in the last few centuries or decades of industrialization and urbanization than they did since our species diverged from Neanderthals.

“The most dramatic gut microbiome change in our evolutionary history is occurring now in modern industrial societies,” Candela told Ars.

Two species, both alike in gut bacteria

Besides underscoring how much biodiversity we’re losing in our own guts, the Neanderthal gut microbiome holds some clues about how our extinct cousins lived.

For instance, the presence of those fiber-fermenting genera like Roseburia, Ruminococcus, and Faecalibacterium told Candela and his colleagues that plants had played an important role in the diet of Neanderthals and our last common ancestors—and probably even earlier members of our genus. That’s a line of evidence that can help supplement what paleoanthropologists know based on the teeth of other hominins, as well as traces of food found at some Neanderthal sites.

And Candela and his colleagues also noticed DNA from genera like Bacteroides, Bifidobacterium, and the brilliantly named Coprococcus, all of which help turn cholesterol into compounds like coprostanol, the fecal biomarker that identified the fecal sediments in the first place. Their presence suggests that Neanderthals needed a bit of help to metabolize cholesterol from foods like animal fats, meat, and eggs. That’s not terribly different from ancient or modern human diets (though modern industrialized populations arguably take the cholesterol thing to a whole new level).

In the end, the world’s only known Neanderthal poop tells us something interesting but not terribly surprising: Neanderthals were a lot like us. “We were expecting this overall, as the two lineages are very close from the evolutionary point of view,” Candela told Ars.

Communications Biology, 2021 DOI:  10.1038/s42003-021-01689-y  (About DOIs).

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