As waves of humans left Africa tens of thousands of years ago, eventually populating the entire planet, they were joined on their world-conquering ride by the trillions of microorganisms that compose the gut microbiome. These bacteria, viruses and fungi in our intestines play essential roles in enabling our bodies to function properly, from digesting fibrous food to making vitamins and training our immune systems.
The microbiome has emerged as a focus of intense study due to evidence that lifestyle impacts its composition, which in turn can affect health. People living in industrialized countries show a profound loss of microbiome diversity compared with people living non-industrialized lifestyles. People in industrialized countries suffer from autoimmune diseases, Type 2 diabetes, obesity and other chronic conditions that are rare among non-industrialized groups, raising the important but still unresolved question of whether microbiome loss contributes to these diseases.
A new study to publish Oct. 7 in Nature and led by Stanford University researchers has attempted to answer the question of whether homo sapiens hosted a characteristic and diverse microbiome going back millennia. Gaining insight into which, if any, long-term residents of the microbiome co-evolved with humans could point to ways to investigate how the loss of microbial diversity through industrialization impacts human biology.
For their study, the researchers conducted the first-ever deep comparison of the microbiomes of the Hadza in Tanzania — one of the world's few remaining hunter-gatherer groups — and the Tsimane, indigenous forager-horticulturalists living in the Bolivian Amazon whose lifestyles have had comparatively limited exposure to industrialization. Although the ancestral human populations that gave rise to the two groups became geographically separated tens of thousands of years ago, the Hadza and Tsimane share over 1,200 bacterial species, nearly 90% of which were identified in the highly diverse Tsimane microbiomes. Most of those species — about 60% — are rare or completely absent in industrialized populations' microbiomes.
Using several complementary population genetics analysis techniques, the researchers estimated when microbial strains separated. For many species, those estimates correspond to the time frame of major prehistoric human migrations out of Africa and into the Americas. The ultimate takeaway: Many microbial lineages in these contemporary populations have deep evolutionary roots extending back through ancient human migrations.
"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," said Justin Sonnenburg , PhD, a professor of microbiology and immunology, the Alex and Susie Algard Endowed Professor, and the study's senior author. "This long-term association has implications for how such recent biodiversity loss in our microbiome may impact our biology and thus our health."
Deep genomic analysis
For the study, the researchers used deep metagenomic sequencing, a method that characterizes the microbes present in a sample by reading out all the letters of the building blocks of DNA present. Millions of small sequences of DNA are generated with overlapping stretches of letters indicating where the small sequences match up into longer sequences. Those long sequences are then compared with databases of microbial genomes to identify the detected organism.
The Tsimane Health and Life History Project team, who are collaborators on the study, had obtained voluntary stool samples from the Tsimane. Sonnenburg and colleagues previously completed a metagenomic sequencing on Hadza samples — reported in a 2023 Cell study — showing, among other findings, that the average Hadza individual has about 750 species in their microbiome, while the average Californian has a mere 250. For the new study, the Stanford University researchers did the first deep sequencing of the Tsimane samples, which had previously been sequenced only at low resolution (in the 2020 Nature Communications study ).
The sequencing efforts enabled the researchers to build a comprehensive census of the microbes in the respective microbiomes, including hard-to-capture, low-abundance species. Overall, the sampled Tsimane individuals hosted about 1,400 different species; they shared a total of 1,231 of these species (about 90%) with the Hadza, according to the new analysis.
"We were really surprised to see that the vast majority of the species in the Tsimane's microbiome correspond with the Hadza's," Sonnenburg said.
Different lifestyles, similar results
Some of that surprise stems from the considerably different diets between the two groups. The Hadza hunt meat from mammals including impala and porcupine, along with birds and fish, and forage for fruits and vegetables including tubers and berries. The Tsimane instead grow much of their food and consume high levels of fiber through plantains, rice, manioc root and corn, along with lean meat from fish, peccary and other forest animals.
Additionally, the two groups have been separated for tens of thousands of years. Despite this geographic and lifestyle separation, the two microbiomes showed a high level of overlap at the species level.
"That made us wonder if there really is a core set of bacterial and other species that traveled with the ancestors of the Tsimane as they migrated around the globe," said Benjamin Good , PhD, the study's senior co-author and an assistant professor of applied physics who specializes in investigating evolutionary dynamics and population genetics of the human gut microbiome.
"Could these bugs have been in continual interaction with us since long before the ancestors of today's Hadza and Tsimane became geographically separated?" Sonnenburg asked. "To answer that, we turned to Ben's team, and what they found blew our minds."
An interwoven biology goes way back
Unpacking the evolutionary history of a microbiome overall has proven daunting given complexities posed by how quickly microbes evolve and the changes a given person's microbiome can undergo from season to season, or based on other aspects of food availability.
Good's group sought to get around these issues. Bacteria complicate evolutionary reconstruction because they not only inherit DNA from their direct ancestors as they clone themselves to reproduce, but also frequently exchange DNA with other strains in a process known as horizontal gene transfer. The researchers therefore looked for several independent genomic signatures to distinguish deep shared ancestry from more recent microbial exchange. Looking at mutation rates in vertically inherited DNA also helped estimate when species diverged from a common ancestor because mutations accumulate at a steady pace, like ticks of a clock.
That analysis squarely indicated that many of the shared bacterial species between the non-industrialized groups' microbiomes have evolutionary histories that trace back over thousands of years. These detailed analyses of genetic isolation of strains produced time estimates consistent with the major human migrations. "We see evidence that these bacteria were present in the ancestors of both the Tsimane and the Hadza, and therefore presumably the ancestors of all of us," Good said.
The researchers said the findings highlight an important hypothesis: If humans interacted with many of these organisms for tens of thousands of years, what happens when industrialization eliminates a large portion of them over just a few generations? Previous work in the field links changes in microbiomes to many disease states. Dramatic changes to our resident microbial populations — attributed to antibiotic exposure; low-fiber, high-fat and -sugar diets of processed food; highly sanitized living conditions; and other factors — could be incompatible with the biology encoded in our human genomes. The biological consequences of this recent biodiversity loss is an important target for future study.
The Stanford University researchers plan to continue investigating the history of our microbiome and its links to health and well-being.
"If these microbes hosted by the Hadza and Tsimane really are part of our evolutionary biology, then those of us in industrialized countries are missing a huge part of what our human genome has potentially adapted to over a vast time period," Sonnenburg said. "We're interested in more fully exploring these long-standing relationships between humans and our gut microbes."
Researchers from the University of Colorado; the University of California, Santa Barbara; the University of Washington; Wake Forest University School of Medicine; Arizona State University; Chapman University; Toulouse School of Economics; Universidad Mayor San Simeon; Veterans Affairs Palo Alto Health System; and Chan Zuckerberg Biohub contributed to the study.
This study was funded by Open Philanthropy, a Stanford Bio-X Bowes Fellowship, the National Institutes of Health/National Institute on Aging (grants R01-AG054442 and R35- GM146949), the National Science Foundation, the Wenner-Gren Foundation, the Thomas C. and Joan M. Merigan Endowment at Stanford University, and the French National Research Agency under the Investments for the Future (Investissements d'Avenir) program.
