Did Industrialization Gut Our Microbiomes? A New Study on Rural Foraging Communities in South America and Africa Hints the Answer Is Yes

The Tsimane grow plantains, rice and root vegetables in the warm, wet Amazonian lowlands of South America. The Hadza gather edible plants and hunt impala across arid Tanzanian plains of Africa. In terms of habitat and diet, the modern forager-horticulturist and hunter-gatherer groups, respectively, bear little in common—which is why researchers were so surprised to find a key overlap in one crucial ecosystem: their guts.

In a study published in the journal Nature on October 7, researchers found an astonishing overlap in the gut microbiomes of the two populations, even though they’re separated by an ocean. Scientists say these rural communities’ guts share few microbial strains with city inhabitants, even those living nearby. The findings suggest that much of the global population has lost a significant portion of their ancestral gut microbiome in the march toward modernity.

Past research hints they can affect our moods, behaviors, and disposition to certain diseases and chronic conditions, like cancer and diabetes. The tiny organisms are also in constant flux: Microbiomes can change based on the season, dietary choices and medicine consumption. Because modern-day guts are responding to a barrage of constant stimuli, Sonnenburg and his colleagues decided to study the pre-modern microbiome by comparing the gut flora of two of the few remaining peoples whose lives are relatively untouched by industrialization.

The researchers compared fecal samples from members of the Hadza and Tsimane communities. Examining the microbial DNA within revealed that the two groups shared more than 1,200 microbial species. Nearly 90 percent of species within the sampled Tsimane individuals were also found in the examined Hadza individuals.

Dating techniques based on the microbes’ mutations suggest the two communities shared a common ancestor that lived around 17,000 years ago. That hints the Tsimane’s lineage acquired much of their microbiome before modern humans migrated to the Americas via the Bering land bridge, which once connected what’s now Russia and Alaska. People began practicing agriculture around 12,000 years ago, leading many to trade their traditional, nomadic hunter-gatherer lifestyles for more stationary ones.

What’s more, comparing both groups’ gut microbiomes with those of industrialized populations revealed a gap: Around 60 percent of the distinct strains shared by the Hadza and the Tsimane are rare or missing in the guts of urbanized folks. That tracks with Sonnenburg’s previous findings; in 2023, he and his colleagues reported that the average Californian resident’s gut had only 277 different microbial species, compared to a Hadza individual’s 730. Sonnenburg says this lack of bacterial diversity—and the accelerated rate at which industrial microbiomes have transformed—might be behind the increased rates of inflammation and disease in industrialized societies.