Scientists have found dramatic differences between gut microbiomes from ancient North American peoples and modern microbiomes, offering new evidence on how these microbes may evolve with different diets.

The scientists analyzed microbial DNA found in indigenous human paleofeces (desiccated excrement) from unusually dry caves in Utah and northern Mexico with extremely high levels of genomic sequencing, says Joslin Assistant Investigator Aleksandar Kostic, PhD, senior author of a Nature paper presenting the work.

Performing genomic analysis more broadly and deeply than previous studies on ancient human gut microbiomes, the study was the first to reveal novel species of microbes in the specimens, says Kostic, who is also an Assistant Professor of Microbiology at Harvard Medical School.

In previous studies of children in Finland and Russia, Kostic and his colleagues showed that children in industrialized regions, who were much more likely to develop type 1 diabetes than those in non-industrialized areas, also had very different gut microbiomes. «We were able to identify specific microbes and microbial products that we believe hampered a proper immune education in early life,» Kostic says. «And this leads later on to higher incidents of not just type 1 diabetes, but other autoimmune and allergic diseases.»

So what would a healthy human microbiome look like before the effects of industrialization? «I’m convinced that you can’t answer that question with any modern living people,» says Kostic, who points that even tribes in extremely remote regions of the Amazon are contracting Covid-19.

Steven LeBlanc, an archeologist formerly with Harvard’s Peabody Museum of Archaeology and Ethnology, came to Kostic with a dramatic alternative source: microbial DNA found in human paleofeces samples that museums have collected from arid environments in the North American Southwest.

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