Hadza (Tanzania) and Tsimane (Bolivia) share 1,231 gut bacterial species despite zero recent contact and completely different diets. Their ancestors split tens of thousands of years ago.
87.4% of Tsimane species also found in Hadza. The kicker: 848 of those 1,231 shared species (60.2%) are rare or extinct in industrialized guts. That's over 600 species we likely lost.
Strain-level mutation analysis shows 85.6% of these species had zero recent genetic exchange between the two populations. Median last common ancestor: 17,090 years ago (±863 years). Compare that to industrial populations: Europe-North America strains diverged only 1,109 years ago, Asia-North America 4,637 years ago. The isolation is real (P < 10⁻⁴).
Species-accumulation curves estimate Hadza guts can host ~2,443 species (CI: 2,385-2,503), Tsimane ~1,590 (1,561-1,620). Average Californian? 277 species. We're running a stripped-down microbiome.
The 17k-year split roughly aligns with human migration into the Americas, not the original out-of-Africa event. Some species like Ruminococcus bromii are still globally common, but most of the 848 are vanishing from industrial populations.
The paper doesn't prove these losses cause modern diseases (allergies, dementia, etc.), just that long co-residence suggests our biology may depend on functions these microbes provided. What those functions are and what replaced them? Still unknown. The sequencing shows who's missing, not what they did.
Data: 351 Hadza stool samples (2013-2014), Tsimane samples via Tsimane Health and Life History Project. Published Nature, October 7, 2026.
87.4% of Tsimane species also found in Hadza. The kicker: 848 of those 1,231 shared species (60.2%) are rare or extinct in industrialized guts. That's over 600 species we likely lost.
Strain-level mutation analysis shows 85.6% of these species had zero recent genetic exchange between the two populations. Median last common ancestor: 17,090 years ago (±863 years). Compare that to industrial populations: Europe-North America strains diverged only 1,109 years ago, Asia-North America 4,637 years ago. The isolation is real (P < 10⁻⁴).
Species-accumulation curves estimate Hadza guts can host ~2,443 species (CI: 2,385-2,503), Tsimane ~1,590 (1,561-1,620). Average Californian? 277 species. We're running a stripped-down microbiome.
The 17k-year split roughly aligns with human migration into the Americas, not the original out-of-Africa event. Some species like Ruminococcus bromii are still globally common, but most of the 848 are vanishing from industrial populations.
The paper doesn't prove these losses cause modern diseases (allergies, dementia, etc.), just that long co-residence suggests our biology may depend on functions these microbes provided. What those functions are and what replaced them? Still unknown. The sequencing shows who's missing, not what they did.
Data: 351 Hadza stool samples (2013-2014), Tsimane samples via Tsimane Health and Life History Project. Published Nature, October 7, 2026.