New research examining the gut microbiomes of two geographically distant Indigenous communities suggests that the trillions of bacteria living inside the human digestive tract may share a deep evolutionary history tied to human migration. The study, published in the journal Nature, compared the gut bacteria of the Hadza people of northern Tanzania with those of the Tsimane people of the Bolivian Amazon, two groups separated by roughly 7,000 miles and an ocean, yet whose internal microbial communities appear strikingly similar.
The Hadza are hunter-gatherers who have inhabited the savanna and woodlands of northern Tanzania for thousands of years, sustaining themselves through foraging, hunting wild game and collecting honey, tubers and berries. Their way of life is often studied by scientists seeking to understand human biology before the rise of agriculture and industrialization. The Tsimane, meanwhile, live in the lowland forests of the Bolivian Amazon, where they practice a mixed subsistence strategy that includes horticulture, fishing, hunting and foraging. Though their environments differ dramatically, both groups live in rural settings with limited access to processed foods, antibiotics and the sanitized conditions typical of modern urban living.
The similarities in their gut microbiomes are significant because they may represent remnants of an ancestral microbial community that traveled with humans as they dispersed across continents. When early humans migrated out of Africa and populated the rest of the world tens of thousands of years ago, they likely carried not only their own genes but also a vast array of gut-dwelling bacteria. Those microbes co-evolved with their human hosts, aiding in digestion, producing vitamins and training the immune system to distinguish between harmful pathogens and benign organisms.
Over the past century, however, industrialization, urbanization, widespread antibiotic use, cesarean births and highly processed diets have dramatically altered the microbiomes of people living in wealthy, industrialized nations. Many bacterial species common in rural, non-industrialized populations are rare or entirely absent in the guts of people living in the United States and Europe. Some researchers refer to this loss as a form of "microbial extinction," and worry it may be linked to rising rates of autoimmune disorders, allergies, obesity and inflammatory diseases.
The new paper adds weight to the idea that the microbiomes of groups like the Hadza and the Tsimane are not simply the product of their local diets and environments, but rather reflect an older, shared heritage. If two groups separated by thousands of miles and thousands of years still harbor similar bacterial communities, that suggests those microbes were present in the common ancestors of both populations before their paths diverged. In other words, the bacteria may have been passengers on the human journey across continents.
Experts say the findings raise important questions about what has been lost as human societies have modernized. If certain gut bacteria have accompanied humans for millennia, their disappearance from industrialized populations could have consequences for health that scientists are only beginning to understand. The gut microbiome is known to influence digestion, metabolism, immune function and even mental health, though the precise mechanisms remain an active area of research.
Studying groups such as the Hadza and the Tsimane offers a rare window into what the human microbiome may have looked like before the widespread changes of the last few hundred years. However, these communities are not frozen in time. Many are increasingly exposed to roads, markets, antibiotics and processed foods, meaning their microbiomes may also be shifting. Researchers face a closing window of opportunity to document microbial diversity while it still exists in something resembling its ancestral form.
The study in Nature highlights the value of comparative research across cultures and continents. By analyzing stool samples and lifestyle data from both Tanzanian hunter-gatherers and Bolivian horticulturalists, scientists were able to identify bacterial strains shared between the groups and assess how those strains differ from those found in people living in industrialized countries. The overlap suggests that a core set of microbes has persisted across vast distances and long stretches of time.
The findings also have implications for understanding human migration itself. Just as geneticists use DNA to trace the movement of ancient peoples around the globe, microbiologists may be able to use gut bacteria as a complementary record of human dispersal. The bacteria people carry can be passed from mother to child and shared within communities, making them potential markers of population history and interaction.
At the same time, the research raises ethical and practical questions. Should scientists attempt to restore lost microbes to people in industrialized societies? If so, which ones, and how? Some researchers have proposed "rewilding" the human gut by introducing bacteria from non-industrialized populations, but such interventions remain highly experimental and carry unknown risks. The new study does not recommend any specific treatment, but it provides a foundation for future work.
For now, the paper underscores how much remains unknown about the microscopic passengers that have accompanied humans on their long journey across the planet. The gut microbiome is a complex, dynamic ecosystem that responds to diet, environment, medication and social contact. Understanding its evolutionary roots may help scientists decipher why some people develop chronic diseases while others remain relatively healthy.
The Hadza and the Tsimane, though separated by an ocean, may be among the last communities whose microbiomes still echo an ancient past. Their similarities offer a glimpse of a shared microbial inheritance that industrialization has largely erased elsewhere. As researchers continue to study these populations, they hope to uncover not only the history of human migration but also clues about how to protect and restore the microbial communities that keep people healthy.
The study, published in Nature, adds to a growing body of evidence that the human relationship with gut bacteria stretches back far beyond the advent of agriculture or written history. It suggests that the microbes living inside us today are not merely a product of modern diets and environments, but living relics of a journey that began in Africa and carried humans to every corner of the Earth.
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