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A study published Oct. 7 in Nature compared gut microbiomes from the Hadza in Tanzania and the Tsimane in the Bolivian Amazon. Researchers found 1,231 bacterial species shared by the groups and estimated that many microbial lineages separated around the period of ancient human migrations. The findings suggest many microbes now rare or absent in industrialized populations have long been associated with humans, but the study does not establish whether their loss causes chronic disease.
A study published Oct. 7 in Nature found that the Hadza of Tanzania and the Tsimane of the Bolivian Amazon share 1,231 gut bacterial species, with genetic estimates suggesting many of their microbial lineages separated during ancient human migrations. The Stanford-led research adds evidence that some gut microbes travelled with human populations over tens of thousands of years, while leaving unresolved whether the loss of these microbes in industrialized societies contributes to chronic disease.
Researchers conducted deep metagenomic sequencing on stool samples from the Tsimane, an Indigenous population of forager-horticulturalists, and compared the results with previously sequenced samples from the Hadza, one of the few remaining hunter-gatherer groups. The method reads DNA from the organisms in a sample, allowing researchers to identify microbes, including species present in small amounts that can be missed by less detailed analysis. The Tsimane samples had previously been sequenced at lower resolution.
The analysis found that the sampled Tsimane hosted about 1,400 microbial species; 1,231 were also identified in the Hadza. Nearly 90% of the Tsimane species therefore overlapped with those in the Hadza, according to the researchers. About 60% of the shared species were rare or completely absent in microbiomes from industrialized populations, the study reported.
The groups have been separated geographically for tens of thousands of years and have distinct diets. The Hadza hunt and forage, while the Tsimane grow much of their food and consume substantial amounts of fiber from foods including plantains, rice, manioc and corn. Using several population-genetics methods, the researchers estimated when microbial strains diverged. For many species, those estimates fell within the broad period of major human migrations out of Africa and into the Americas. These are genetic estimates, not direct observations of microbes moving with specific people.
The findings suggest that some gut microbes have deep historical ties to human populations, rather than reflecting only recent diet or local environment. Similarities between the Hadza and Tsimane persisted despite their different foodways and long geographic separation, supporting the possibility that certain microbial lineages were passed between people over many generations.
The result also gives researchers a way to investigate the decline in microbial diversity seen in industrialized populations. The study reports that many species shared by the Hadza and Tsimane are scarce or absent in industrialized microbiomes. That difference matters because gut microbes help digest food, produce vitamins and interact with the immune system. However, the study does not show that losing the microbes causes autoimmune disease, Type 2 diabetes, obesity or other chronic conditions. Whether microbiome loss contributes to those health patterns remains an open research question.
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How the Populations Were Compared
The research builds on earlier work by the Stanford team. A 2023 study in Cell reported that the average Hadza individual had about 750 microbial species, compared with about 250 in the average Californian individual. Those figures come from that earlier study and should not be read as a direct measurement of the new comparison. The Tsimane samples had been examined in a 2020 Nature Communications study, but at lower resolution than in the new analysis.
For this report, collaborators with the Tsimane Health and Life History Project collected voluntary stool samples. The Stanford researchers then used deep sequencing to make a broader census of the microbes present. The comparison focuses on species and genetic relationships in two contemporary populations; it does not provide a complete record of ancient human microbiomes or establish the exact route by which each microbe spread.
““Our study establishes that the hundreds of bacterial species that are rare or missing in industrialized microbiomes were ancient companions of ours as we migrated around the globe, likely passed from generation to generation for millennia.””
— Justin Sonnenburg, Stanford professor of microbiology and immunology and the study’s senior author
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What the Genetic Dates Cannot Show
The timing estimates do not prove precisely when or how each microbial lineage entered either population. They indicate when strains may have diverged based on genetic comparisons, and the researchers say many estimates align with broad periods of prehistoric migration. The available findings do not establish that every shared species travelled with migrating humans, or rule out other routes of transmission and ecological influences.
The study also does not determine whether the absence of these microbes in industrialized populations directly contributes to illness. Researchers have identified a contrast in microbial diversity, but the health consequences and possible causal links remain uncertain. The report does not provide evidence that restoring particular species would prevent or treat chronic conditions.
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Testing Microbial Loss and Health
The findings provide a basis for further research into how microbial diversity changed as human communities adopted industrialized lifestyles, and whether those changes affect human biology. Researchers would need to connect microbial histories and present-day differences to health outcomes before drawing conclusions about disease risk or possible interventions.
The study’s immediate contribution is a more detailed comparison of two populations whose lifestyles have had comparatively limited exposure to industrialization. Further work could test whether similar patterns appear in other populations and clarify which microbial lineages are widespread, how they were transmitted, and what roles they play. No follow-up results or clinical recommendations are reported in the supplied study account.
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Key Questions
Which populations did the researchers compare?
The study compared gut microbiomes from the Hadza in Tanzania and the Tsimane in the Bolivian Amazon. The Hadza are hunter-gatherers; the Tsimane are forager-horticulturalists.
How many microbial species did the groups share?
The researchers reported 1,231 shared species. The sampled Tsimane hosted about 1,400 species in total, so the shared count represented nearly 90% of the Tsimane species identified in the analysis.
Do the results prove that microbes migrated with humans?
No. Genetic estimates for many microbial strains were consistent with the broad timeframe of ancient human migrations. That supports the possibility of long-term association and transmission, but does not directly prove the route or timing for every species.
Does the study show that losing gut microbes causes chronic disease?
No. The study describes microbial differences between populations and notes that many shared species are rare or absent in industrialized microbiomes. It does not establish that this loss causes autoimmune disease, Type 2 diabetes, obesity or other chronic conditions.
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