In 2017, in a paper Science promoted on its cover, Dr. Justin Sonnenburg, Mr. Leach and others compared microbes in the guts of 18 populations in 16 countries. Their study showed a clear distinction between the microbes in people living in industrialized societies and those living in what the investigators called “more traditional” societies, with a particular focus on the Hadza in Tanzania.
“That really clearly shows there are some families of bacteria that are super abundant in all these traditional populations around the world that are rare or extinct in Western populations,” said Dr. Sonnenburg, an immunologist and microbiologist at Stanford University. “That said to us: There were microbes that have lived in humans for hundreds of thousands or probably millions of years, even before modern humans arose, but as populations industrialized we lost those microbes.”
In a 2018 paper in Cell, Dr. Martin Blaser, a professor of the human microbiome at Rutgers, made the case for rewilding: Because of widespread antibiotic use and diets laden with processed foods and lacking fiber, the human microbiome in industrialized societies increases susceptibility to a variety of diseases.
“Restoration of the human microbiome must become a priority for biomedicine,” he wrote.
But how representative are these samples of a true ancestral microbiome, if indeed there is such a thing?
“Today there is no such thing as a truly isolated, uncontacted community,” Dr. Kostic said. To see ancient microbiomes, he said “we really need to go back in time.”
He and his colleagues, using modern DNA sequencing techniques, managed to do just that. They obtained eight samples of human paleofeces from arid caves and rock shelters in the Southwestern United States and Mexico and reconstructed some of their microbial genomes. The microbes they found, Dr. Kostic said, resembled those of people in nonindustrialized societies.
Those microbes helped people digest a wide variety of fibrous foods in huge quantities. Hunter-gatherers eat more than 50 grams of fiber each day, Dr. Kostic said, while the typical American eats about 10 to 15 grams of fiber a day.