Study Links Industrialization to Significant Loss of Ancestral Gut Microbes

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The short version

• Genetic analysis shows Tsimane and Hadza communities share over 1,200 microbial species despite geographic separation.
• Approximately 60 percent of these ancestral strains are rare or missing in the guts of people living in industrialized societies.
• Scientists debate whether this loss of microbial diversity contributes to rising rates of chronic disease in modern populations.

A new study published in Nature suggests that the transition to modern, industrialized lifestyles has led to a substantial decline in the diversity of gut bacteria among human populations. Researchers compared the digestive microbiomes of two distinct rural groups: the Tsimane people of the Amazonian lowlands in South America and the Hadza hunter-gatherers of Tanzania in Africa. Despite living on different continents with vastly different diets and environments, these communities exhibit a striking similarity in their gut flora.

The analysis revealed that the Tsimane and Hadza share more than 1,200 microbial species. Nearly ninety percent of the bacterial species found in the Tsimane samples were also present in the Hadza individuals. This overlap is particularly notable given the geographic distance between the two groups and their differing subsistence strategies, with the Tsimane practicing horticulture and the Hadza relying on foraging and hunting.

Genetic dating techniques applied to the microbial DNA indicate that these shared bacteria likely originated from a common ancestor approximately 17,000 years ago. This timeline suggests that the Tsimane lineage acquired much of this microbiome before modern humans migrated into the Americas via the Bering land bridge. The findings imply that these microbial communities represent an ancestral baseline that has persisted in isolated populations for millennia.

In contrast to these rural groups, individuals living in industrialized settings possess significantly fewer of these ancient bacterial strains. The study found that around sixty percent of the distinct species shared by the Hadza and Tsimane are either rare or completely absent in the guts of urban dwellers. Previous research by the same team highlighted this disparity, noting that an average resident of California hosts only about 277 microbial species, compared to roughly 730 found in a single Hadza individual.

Justin Sonnenburg, a microbiologist at Stanford University and co-author of the study, argues that human biology may have evolved to expect a specific set of microbial functions. He suggests that the rapid loss of gut biodiversity could make it difficult for modern bodies to adjust, potentially contributing to increased rates of inflammation and chronic diseases such as diabetes and cancer. The shift toward processed foods low in fiber and high in sugar and fat appears to favor different microbial communities than those our ancestors relied upon.

However, not all experts agree that the loss of ancestral microbes is inherently harmful. Andrew Moeller, an evolutionary biologist at Princeton University who was not involved in the research, points out that modern microbiome profiles might be better adapted to contemporary industrialized lifestyles. He notes that it remains unclear whether retaining these ancient taxa would actually improve health outcomes for people living in cities today.

The study underscores the vast gaps in current scientific understanding regarding the role of gut bacteria in human health. While the research does not definitively prove that ancestral microbiomes are superior, it highlights how little is known about the microorganisms that inhabit our bodies. Marie-Claire Arrieta, a microbiome scientist at the University of Calgary, emphasizes that much work remains to be done to fully comprehend these complex ecosystems.

As humanity continues to modernize, the implications of this microbial shift remain uncertain. The findings provide a clearer picture of what has been lost in the march toward industrialization but do not yet offer solutions for restoring diversity or mitigating potential health risks. Future research will need to determine whether interventions can safely reintroduce beneficial strains or if the body can adapt to its new microbial reality.

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