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A 2026 study in Nature found that Tsimane adults in Bolivia and Hadza participants in Tanzania shared hundreds of gut microbial species that are rare or absent in available industrialized-population datasets. The findings support the idea that some microbes have accompanied human populations over long periods. They do not show that industrialization alone caused those microbes to disappear, or that losing them causes a particular disease.
What the study found
Researchers compared gut microbial genomes from two distinct populations: the Tsimane, Indigenous forager-horticulturalists in Bolivia, and the Hadza, hunter-gatherers in Tanzania. They found 1,231 species in common, equal to 87.4% of the 1,408 species identified in the Tsimane cohort. Of those 1,408 Tsimane species, 848—60.2%—were rare or absent in fecal microbiome datasets from industrialized populations.
Those percentages describe species detected across study datasets. They do not mean that every Tsimane or Hadza participant carried every shared species, or that the 848 species are universally absent from people living in industrialized settings. The comparison is with the industrialized-population data available to the researchers.
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How researchers built the comparison
The team used deep metagenomic sequencing, which reads genetic material from the many organisms in a sample rather than requiring each microbe to be grown separately. From 133 stool samples collected from 85 Tsimane adults in 2009 and 2012–2013, the researchers assembled 12,746 metagenome-assembled genomes (MAGs), representing 1,408 bacterial and archaeal species. They compared these with 32,034 MAGs from 137 Hadza participants.
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| Study detail | Tsimane cohort | Hadza cohort |
|---|---|---|
| Population and location | Indigenous forager-horticulturalists in Bolivia | Hunter-gatherers in Tanzania |
| Participants | 85 adults | 137 participants |
| Stool samples | 133, collected in 2009 and 2012–2013 | Not stated in the study summary |
| Metagenome-assembled genomes | 12,746 | 32,034 |
| Species identified | 1,408 | Not stated in the study summary |
The populations are useful for examining microbial diversity beyond the industrialized datasets, but they are not interchangeable examples of a single “traditional” lifestyle. They live in different regions and have distinct subsistence practices and histories. The study’s population-genetic analyses also accounted for microbial recombination, which can complicate attempts to infer how strains are related.
What the genomes suggest about human history
The authors used genetic patterns in present-day microbes to infer that many species may have long histories of association with humans. Some estimated strain-divergence patterns align with major prehistoric human migrations. That is an evolutionary interpretation of contemporary genomic data—not a direct record of microbes moving alongside ancient people. The study did not sequence ancient human microbiomes to observe those migrations.
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Other explanations remain possible. More recent acquisition from the environment or through human contact could also help account for microbial similarities and differences. Distinguishing those possibilities requires care: shared species do not, by themselves, establish when or how the microbes entered each population.
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No. The results show that many species found in the Tsimane cohort were rare or absent in the industrialized-population fecal microbiome datasets used for comparison. The study did not follow the same people as their communities industrialized, nor did it isolate industrialization as the cause of a species’ absence. Differences in geography, diet, ecology, population history, sampling and available datasets may all matter.
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“Rare or absent” is therefore a description of the comparison, not proof of universal absence or a causal explanation. The headline idea that industrialization “gutted” microbiomes captures a concern the study raises, but it is stronger than what this cohort comparison alone can establish.
What the findings mean for health—and what they do not
The study documents microbial diversity and offers clues about microbial evolutionary history. It does not establish that losing any of the identified species causes a specific health condition, quantify a resulting disease burden, or show that restoring them would improve health. The authors say the health consequences remain uncertain.
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No supplement, probiotic, consumer microbiome test or other intervention was tested. The findings are not a basis for trying to recreate the Tsimane or Hadza microbiome with a product. Knowing that a species is uncommon in one comparison is not enough to establish that it is beneficial, safe to introduce, or appropriate for an individual.
Why the result matters despite its limits
The work expands the picture of human gut microbes beyond populations commonly represented in industrialized-country datasets. The high species overlap between the Tsimane and Hadza cohorts, alongside the rarity or absence of many Tsimane species in industrialized-population data, gives researchers a basis for asking how human migration, local environments and changing ways of life shape microbial communities.
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As study co-senior author Benjamin Good put it, “That made us wonder if there really is a core set of bacterial and other species that traveled with the ancestors of the Tsimané as they migrated around the globe.” It is a research question prompted by the genomic patterns, not proof of a single, fixed human “core” microbiome. The Nature paper’s central contribution is evidence of shared species and evolutionary clues; the causes of present-day differences and their implications for health remain open questions.
Sources: Nature, “Prehistoric global migration of vanishing gut microbes with humans” (2026); The Current at UC Santa Barbara, “Microbiome study reveals ancient gut connections between Africa and South America” (2026).
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