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

Two groups—the Tsimane forager-horticulturists in Bolivia and the Hadza hunter-gatherers in Tanzania—remarkably share more than 1,200 gut microbe species. However, around 60 percent of them are rare or absent in people living in industrialized places, according to researchers

Gabby Shell | Editorial intern

October 13, 2026 9:00 a.m.

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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. More striking? 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. 

“Our human genomes may have come to expect a certain set of microbes and functions,” study co-author Justin Sonnenburg, a microbiologist at Stanford University, tells NPR’s Pien Huang. “When you start to lose biodiversity in your gut, there may be big issues for your human biology to adjust to and accommodate.”

Our gut microbiomes are expansive—and still largely unexplored—systems of bacteria, viruses fungi and other microorganisms that help run our digestive systems. 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.

“We were really surprised to see that the vast majority of the species in the Tsimane’s microbiome correspond with the Hadza’s,” Sonnenburg says in a statement. 

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.

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. 

“How bad could this be, the fact that we changed our microbiomes so much?” Sonnenburg tells Carl Zimmer at the New York Times. “This study, I think, points to the fact that it could be pretty bad.” 

For example, certain bacterial strains may have evolved to instruct our immune systems, synthesize necessary compounds or protect us from disease, according to the outlet. But as humanity modernized—and diets shifted toward highly processed foods low in fiber and high in sugar and fat—many of these strains gave way to new microbes that might be different from what human bodies are programmed to expect, Sonnenburg says. 

But not all scientists are convinced the microbial disparity is cause for concern. Andrew Moeller, an evolutionary biologist at Princeton University who was not involved in this research, tells NPR it’s possible that modern microbiome profiles may be more ideal for an industrialized lifestyle. 

“From a health perspective, is it good or deleterious that industrialized humans have lost a lot of ancestral microbial taxa [groups]?” he says. “We actually don’t know.”

While this new research doesn’t show whether these ancient microbiomes are superior to modern ones, it does underscore the vast amount of research yet to be done to understand the microbe communities that live inside us, Marie-Claire Arrieta, a microbiome scientist at the University of Calgary in Canada, tells the Times. Arrieta was not involved in the research. 

“The message that we should go back to ancient microbiomes doesn’t make a lot of sense,” she says. “But, for sure, they’re important to study to understand some of these microbial functions that have been lost.”