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Gut Microbiome Differences Highlighted Between Industrialized, Non-Industrialized Populations

NEW YORK – Researchers have examined the gut microbiomes of one of the last hunter-gatherer groups, comparing them to the microbiomes of people from industrialized areas.

The Hadza are among the last hunter-gatherer groups in the world who forage on wild food and practice no cultivation or animal husbandry. In a study published in Cell on Wednesday, researchers from Stanford University studied fecal samples obtained from Hadza hunter-gatherers and found 124 gut-resident species in their gut microbiomes that were absent in samples from people who live in industrialized places.

"This unparalleled view of the Hadza gut microbiome provides a valuable resource, expands our understanding of microbes capable of colonizing the human gut, and clarifies the extensive perturbation induced by the industrialized lifestyle," corresponding authors Erica and Justin Sonnenburg, researchers from Stanford, and their colleagues wrote in their paper. The findings could also aid the understanding of how the gut microbiome affects human health and diseases, they noted.

For this study, the researchers performed ultra-deep metagenomic sequencing on 351 fecal samples from 167 Hadza hunter-gatherers and populations in Nepal and California who also have lived in relatively unindustrialized areas. By including these Nepali and Californian populations, the authors noted that they could make microbiome comparisons across lifestyles without the need for sequence rarefaction.

In their analysis, the researchers found 91,662 bacterial, archaeal, bacteriophages, and eukaryotic genomes. Close to 44 percent of these genomes come from species that are absent from the Unified Human Gastrointestinal Genome (UHGG) database and the Metagenomic Gut Virus catalog, which mainly have data from people from industrialized regions.

Among the eukaryotic genomes recovered from the Hadza gut microbiome, the researchers found a large and complete genome of a stingless bee, the honey and larvae of which the Hadza are known to consume. Four other genomes present in the Hadza gut microbiomes are previously uncharacterized Amoebae and Trepomonas genomes.

Meanwhile, a total of 52 bacterial strains from the Hadza samples were isolated and subjected to whole-genome sequencing. These genomes belong to 31 different bacterial species, 18 of which have no previously cultivated representative and nine of which are not present in the UHGG database.

"Overall, our results conclusively show that the differences between industrialized and non-industrialized microbiomes go well beyond simple taxonomic membership and diversity," the authors noted.

Lifestyle and diet could account for some of the gut microbiome differences seen between people living in industrialized versus non-industrialized regions. The researchers noted that consumption of highly processed foods, high rates of antibiotic administration, birth via cesarean section, sanitation of the living environment, and reduced physical contact with animals and soil have been hypothesized to decrease microbiome diversity among people living in industrialized areas. "These aspects are absent from the lifestyle of non-industrialized human populations, including hunter-gatherers, who harbor extremely high microbiome diversity," they wrote.

The researchers added that extending deep metagenomic sequencing to other populations will enable a better understanding of which microbes traveled with, were lost in, or were gained in human populations as they spread around the planet, insights that could potentially help understand which microbes' species and functions are beneficial or detrimental to human health.