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A study led by Stanford researchers found that the Hadza of Tanzania and the Tsimane of Bolivia share more than 1,200 gut bacterial species, despite living far apart and having different diets. Genetic analyses suggest that many of the shared microbial lineages separated around the time of major prehistoric human migrations. The findings do not establish whether losing these microbes causes disease in industrialized populations.
A Stanford-led study published October 7 in Nature found extensive overlap between the gut bacteria of the Hadza in Tanzania and the Tsimane in Bolivia, with genetic analyses suggesting that many shared microbial lineages have roots in prehistoric human migrations. The finding offers evidence that microbes accompanied human populations as they spread across the globe, while leaving unresolved whether the loss of many of these bacteria in industrialized populations contributes to chronic disease.
Researchers used deep metagenomic sequencing to analyze stool samples from the Tsimane, an Indigenous population of forager-horticulturalists, and compare them with previously sequenced samples from the Hadza, a hunter-gatherer group. The method reads DNA from a sample to identify microbial species, including organisms present at low abundance that can be missed by less detailed sequencing.
The analysis identified about 1,400 microbial species among the sampled Tsimane individuals. More than 1,200 species—reported as about 90% of the total—were also found in the Hadza. The researchers said roughly 60% of those shared species are rare or absent in microbiome samples from industrialized populations.
Using several population-genetics methods, the team estimated when microbial strains diverged. For many species, the estimates were consistent with the time frame of major human migrations out of Africa and into the Americas. These are estimates from genetic comparisons, not direct observations of microbes traveling with particular people.
The results add evidence that some gut microbes have been associated with human populations over long periods, and that present-day differences in microbiomes may reflect more than recent diet or geography. The researchers argue that the findings can help identify microbial species that were widespread among people living outside industrialized settings but are now uncommon in industrialized populations.
That matters because gut microbes help digest food and produce vitamins, and interact with the immune system. However, this study compared microbial communities and estimated their evolutionary histories; it did not test whether missing species cause autoimmune disease, Type 2 diabetes, obesity or other conditions. Whether microbiome loss contributes to those health differences remains an open research question.
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Comparing Hadza and Tsimane Samples
The Hadza and Tsimane live on different continents and have distinct food systems. The Hadza hunt and gather foods including meat, fish, tubers, fruit and berries. The Tsimane grow much of their food, including plantains, rice, manioc and corn, and also eat lean meat and fish. Their ancestral populations became geographically separated tens of thousands of years ago.
The Stanford team had previously reported deep sequencing of Hadza samples in a 2023 Cell study. Earlier Tsimane samples had been sequenced at lower resolution in a 2020 Nature Communications study. The new work included the first deep sequencing of the Tsimane samples, allowing a more detailed comparison of the two groups. Tsimane samples were collected voluntarily by the Tsimane Health and Life History Project team, which collaborated on the research.
“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 senior author
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Limits of the Migration Evidence
The study’s timing comes from genetic analyses of microbial strains. It does not directly trace individual organisms through specific migration routes, and the estimates do not establish exactly when or how each species reached the two populations. The reported overlap also applies to the groups and samples studied; it does not show that every Hadza or Tsimane person carries every shared species.
The findings do not establish why industrialized populations have fewer of these microbes, or whether that difference causes health problems. The source report does not give the sample size, detailed estimates for individual species, or results from a clinical test of health outcomes. Further work is needed to distinguish effects of industrialization, diet and other factors.
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Further Work on Microbiome Loss
The study provides a comparative dataset and a basis for investigating how long-term human-microbe associations changed as populations adopted industrialized lifestyles. The next questions are whether the rare or missing species have measurable effects on human biology, what factors explain their decline, and whether findings from these communities hold across a wider range of populations.
The material available with the report does not specify a next publication date or follow-up trial. For now, the central result is a genetic comparison: many gut bacterial species found in the Hadza and Tsimane appear to have lineages whose histories overlap with the period of ancient human migrations.
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Key Questions
What did the study find?
Researchers found that the Hadza and Tsimane share more than 1,200 gut microbial species. Genetic analyses suggested that many shared bacterial lineages have deep histories consistent with major prehistoric human migrations.
Does this prove gut microbes traveled with humans?
The study supports that interpretation through genetic comparisons and estimated divergence times. It does not directly observe microbes traveling with people or establish a specific route for each species.
The researchers reported that about 60% of the shared species are rare or completely absent in industrialized populations’ microbiomes. That finding does not mean every industrialized person lacks those species.
Does the study show that losing these microbes causes disease?
No. The study did not test whether microbial loss causes chronic illness. The relationship between microbiome diversity and conditions such as diabetes or autoimmune disease remains unresolved.
Source: rss
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