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A study published in Nature compared gut microbes from the Hadza of Tanzania and the Tsimane of Bolivia, finding they share more than 1,200 bacterial species despite long geographic separation and different diets. Genetic analyses suggest that some microbial lineages separated around the periods of prehistoric human migrations, although the findings do not establish that microbiome loss causes chronic disease.
A Stanford-led study published Oct. 7 in Nature found that the Hadza of Tanzania and the Tsimane of Bolivia share more than 1,200 gut bacterial species, with genetic analyses suggesting that some microbial lineages separated around the time of ancient human migrations. The results offer evidence that a substantial set of gut microbes may have traveled with human populations over millennia, but do not establish whether losing those microbes causes health problems.
The researchers compared gut microbiomes from two Indigenous populations with lifestyles that have had comparatively limited exposure to industrialization: the Hadza hunter-gatherers and the Tsimane forager-horticulturalists. The groups’ ancestral populations became geographically separated tens of thousands of years ago. Their diets differ, yet the study found that they shared 1,231 bacterial species, about 90% of the species identified in the Tsimane samples.
About 60% of the shared species are rare or absent in the microbiomes of people in industrialized populations, according to the report. The team used deep metagenomic sequencing, which reads DNA from the organisms present in stool samples, to identify microbes, including species that can be difficult to detect when they are present in low numbers.
Using several population-genetics methods, the researchers estimated when microbial strains diverged. For many species, those estimates fell within time frames associated with major prehistoric human migrations out of Africa and into the Americas. This is evidence consistent with long-term association between people and these microbes; the study does not directly trace individual bacteria through ancient human remains or prove exactly how each species moved between populations.
The findings add a long historical perspective to research on the human gut microbiome. If some microbial lineages have accompanied human populations for many generations, their scarcity in industrialized populations may reflect a relatively recent change in a much older relationship. That possibility gives researchers a basis for asking which microbes were once common and what roles they may have played.
The issue matters because gut microbes take part in processes such as digesting fibrous foods, producing vitamins and training the immune system. People in industrialized countries have been found to have less microbiome diversity than people living non-industrialized lifestyles, while chronic conditions including autoimmune diseases, Type 2 diabetes and obesity are less common among some non-industrialized groups. Those patterns do not show that reduced microbial diversity causes the health differences. The study identifies historical and biological questions for further research, not a demonstrated explanation for disease.
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How Researchers Compared Populations
The new analysis builds on earlier work by members of the Stanford team. A 2023 Cell study reported that the average Hadza participant had about 750 microbial species in their gut microbiome, compared with about 250 in an average Californian. The Tsimane samples had previously been sequenced at lower resolution in a 2020 study; the new work used deeper sequencing to produce a more detailed comparison.
The Tsimane Health and Life History Project team collected voluntary stool samples from Tsimane participants. Deep metagenomic sequencing generates many short DNA reads, which researchers assemble and compare with microbial genome databases to identify organisms. Comparing the resulting microbial populations allowed the team to assess shared species and estimate how strains are related over time. The study compares present-day samples; its inferences about ancient history come from genetic analyses rather than direct sampling of prehistoric guts.
“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, the study’s senior author and a Stanford professor of microbiology and immunology
What the Study Cannot Establish
The genetic estimates connect many microbial lineages to time frames associated with human migrations, but they do not establish the exact route or mechanism by which each species spread. The findings also do not show that every shared microbe was passed directly from parent to child, or that the same species were present continuously in every generation.
Most important for health, the study does not determine whether the loss of these microbes in industrialized populations contributes to chronic disease, or whether differences in diet, environment, lifestyle or other factors explain the patterns. The source material does not provide the number of participants or enough detail to assess how representative the samples are of either population. Those limits matter when interpreting a comparison of two groups as evidence about human microbiomes worldwide.
Questions for Follow-Up Research
The immediate next step is further research into which shared microbial lineages are consistently found across populations and how their histories can be tested with additional samples and methods. Researchers will also need to examine whether these microbes have measurable effects on human biology, and whether those effects differ with diet or other conditions.
The study’s findings do not, on their own, support a specific intervention or medical recommendation. For now, the central development is evidence that many microbes common in the Hadza and Tsimane may have deep evolutionary histories linked to human population movements. Whether their reduced presence in industrialized microbiomes has consequences for health remains an open question.
Key Questions
What did the study find?
The analysis found that the Hadza and Tsimane share 1,231 bacterial species. Genetic analyses suggest that many of the lineages may have separated around periods of prehistoric human migration.
Does this prove gut microbes migrated with humans?
The results are consistent with some microbial lineages having moved alongside human populations over time. The study inferred their histories from genetic data; it did not directly observe ancient migrations of microbes or establish the route taken by each species.
Are these microbes missing from everyone in industrialized countries?
No. The report says about 60% of the shared species are rare or completely absent in industrialized populations’ microbiomes. It does not say that every person in an industrialized country lacks them.
Does the study show that losing gut microbes causes disease?
No. It describes differences in microbiome diversity and raises questions about possible effects on health, but it does not establish that microbial loss causes autoimmune disease, Type 2 diabetes, obesity or other chronic conditions.
Source: rss
