2,000-year-old poop reveals mass extinction of never-before-seen bacteria in the human gut

BOSTON, Mass. — It doesn’t take a lot of research to figure out that life thousands of years ago was much different than it is today. While the human body hasn’t changed much over the course of time, a new study finds our gut health certainly has. Researchers with the Joslin Diabetes Center say an analysis of fossilized feces samples reveals human gut bacteria is much less diverse today than it was in the distant past.

In fact, the study finds what some could call an “extinction-level event” of the human microbiome. Microbial DNA from the waste of indigenous humans in North America dating back nearly 2,000 years revealed species of gut microbes which don’t even exist in today’s world.

In previous studies, Kostic’s team discovered that children living in industrialized regions were much more likely to develop type 1 diabetes in comparison to kids in non-industrialized areas. Their gut microbiome, the healthy balance of trillions of bacteria and other organisms in the digestive tract, also developed differently.

“We were able to identify specific microbes and microbial products that we believe hampered a proper immune education in early life,” says Joslin Assistant Investigator Aleksandar Kostic, PhD, in a media release. “And this leads later on to higher incidents of not just type 1 diabetes, but other autoimmune and allergic diseases.”

So what does this mean for humans living in the pre-industrial world?

“I’m convinced that you can’t answer that question with any modern living people,” Kostic says.

The researcher adds scientists can’t even rely on studies of human tribes in remote regions today since even those populations are contracting modern viruses like COVID-19.

Shocking revelations about ancient gut health

To work around this, archeologist Steven LeBlanc proposed examining DNA of human paleofeces (ancient poop samples) collected by museums over the years. These samples come from arid regions and dry caves in Utah and Mexico which preserved them over the centuries.

Kostic and graduate student Marsha Wibowo compared the DNA from eight ancient gut samples to the DNA from 789 modern samples. Over half of the modern gut samplings come from people eating an industrialized “Western” diet. The rest belong to people eating non-industrialized foods, typically grown in their local communities.

Results show some striking differences in gut diversity in the ancient world, with some bacteria no longer existing in modern human diets. Kostic notes Treponema succinifaciens “is not in a single Western microbiome that we analyzed, but it’s in every single one of the eight ancient microbiomes.”

Study authors add the microbiome fossils do match up a little more with the modern non-industrial diet. However, Wibowo discovered nearly 40 percent of the ancient microbial species had never been seen by scientists before.

What is causing the gut microbiome to change so much?

“In ancient cultures, the foods you’re eating are very diverse and can support a more eclectic collection of microbes,” Kostic speculates. “But as you move toward industrialization and more of a grocery-store diet, you lose a lot of nutrients that help to support a more diverse microbiome.”

The study finds ancient microbiomes also had higher levels of transposases, changeable portions of DNA which can shift location in the genome.

“We think this could be a strategy for the microbes to adapt in an environment that shifts a lot more than the modern industrialized microbiome, where we eat the same things and live the same life more or less year-round,” Kostic explains. “Whereas in a more traditional environment, things change and microbes need to adapt. They might use this much larger collection of transposases to grab and collect genes that will help them adapt to the different environments.”

Additionally, the feces fossils revealed ancient humans had fewer genes tied to antibiotic resistance in their guts. They also carried fewer genes that create proteins which damage the mucus layer lining the intestines. When poor gut health in modern times causes this lining to degrade, it produces inflammation and eventually leads to disease.

The study appears in the journal Nature.

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About the Author

Chris Melore

Chris Melore has been a writer, researcher, editor, and producer in the New York-area since 2006. He won a local Emmy award for his work in sports television in 2011.

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