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Archeological Fecal Samples Indicate Ancestral Human Gut Microbiome Resembles That of Modern, Rural Humans

NEW YORK (GenomeWeb News) – Archeological samples of human feces dating back more than a thousand years indicate that ancestral human gut microbiomes more closely resemble the gut microbiomes of modern humans living in rural communities than those of modern, cosmopolitan humans, researchers led by the University of Oklahoma's Cecil Lewis reported in PLOS One yesterday.

By having a better understanding of the makeup of the ancestral human gut microbiome, the researchers said they will be better positioned to gauge how the gut microbiome has evolved, how a modern lifestyle and its accoutrements have affected the gut microbiome, and whether those changes have contributed to disease.

"It is becoming accepted that modern aseptic and antibiotic practices are often beneficial, but come with a price, such as compromising the natural development of our immune system through changing the relationship we had with microbes ancestrally. What is unclear is what that ancestral state looked like," Lewis said in a statement. "This paper demonstrates that we can use ancient human biological samples to learn about these ancestral relationships, despite the challenges of subsequent events like degradation and contamination."

By pyrosequencing the 16S rDNA V3 regions of microbial samples obtained from human feces found at archeological sites, Lewis and his colleagues were able to begin to get a glimpse of what that ancestral human microbiome may have contained. The fossilized fecal samples, or coprolites, came from three distinct environments — Hinds Cave in the southwest US, Caserones in northern Chile, and Rio Zape in northern Mexico. The sites are 8,000 years old, 1,600 years old, and 1,400 years old, respectively.

In their Venn-Euler diagram and principal component analyses of the sequencing data generated, the researchers reported that the microbiomes of coprolites obtained from the same sites were more similar to each other than to the coprolites from other sites, and that the coprolite samples had varying degrees of similarity to the modern human gut microbiome and the modern primate gut microbiome.

Using a Bayesian approach, Lewis and his team compared the coprolite microbiome data to other published gut microbiome data — including data from Ötzi the Iceman and an Austrian soldier found frozen in a glacier after 100 years — as well as to gut, mouth, and skin microbiome data from modern humans living in rural Africa or US cities and to soil and compost microbiomes.

The Rio Zape coprolite microbiome, the authors noted, was similar to the gut microbiomes of modern children living in rural Africa, while the Caserones coprolite microbiome resembled the microbial community of compost. The Hinds Cave microbiome did not resemble any other microbiome. Ötzi the Iceman and the Austrian soldier's microbiomes were also similar to those of children living in rural Africa.

"The results from Rio Zape cave deposit were consistent with the pattern observed in rare and pristine samples retrieved from permafrost mummies," Lewis and his colleagues wrote, adding that "[i]t is unclear whether the results from Hind's Cave and Caserones reflect different preservation conditions, depositional process, or unique gut microbiomes."

Additionally, data from the Rio Zape samples suggested to the researchers that those coprolites came from a child. One Rio Zape sample contained Bifidobacterium, which are commonly found in breast-fed infants, while another had spirochetes, which are also found in children living in rural Africa, though not in cosmopolitan children or adults. Archeological evidence also indicated that children were buried at the site.

All in all, the researchers wrote that their findings indicate that modern life has taken its toll on the human gut microbiome and its composition.

"The analyses suggest that ancient microbiomes are different than the current cosmopolitan human microbiomes and are more similar to rural microbiomes," the authors concluded. "Our results suggest that the most dramatic change to the gut microbiome in the human ancestral line has been the modern transformation of the human condition in cosmopolitan populations."