Thousands of kilometers and an ocean separate the Tsimané of the Bolivian lowlands from the Hadza of Tanzania. Their ancestors separated tens of thousands of years ago. Their diets are not similar. Yet their gut microbiomes are surprisingly similar, according to a study published in Nature by researchers at UC Santa Barbara and Stanford University.
The Hadza are one of the last hunter-gatherer groups on Earth. They hunt impala and kudu, catch birds and fish, and gather tubers and berries. The Tsimané are indigenous farmer-gatherers of the Bolivian Amazon. They grow plantains, rice, cassava and corn and eat lean meat from fish, peccary and other forest animals. Both groups live with little industrial influence.
The team carried out the first deep sequencing of stool samples from Tsimané. Previous work had only sequenced them at low resolution. Deep metagenomic sequencing reads all of the DNA in a sample. It divides DNA into millions of short pieces, aligns the overlaps, and compares the longest segments to databases of known microbial genomes. This method makes it possible to detect rare and low-abundance species that other tools miss.
The Tsimané are home to approximately 1,400 intestinal species in total. They share 1,231 with the Hadza, or about 90 percent. About 60 percent of these common species are rare or absent in populations of industrialized societies. Previous research has found that the average Hadza person is home to around 750 species. The average Californian is home to about 250.
So why do two groups with different foods and homes share so much? Not because both live in rural areas where antibiotics are limited, says Michael Gurven, an anthropologist at UCSB. His argument is that humans have carried these bacteria for hundreds of generations.
Stanford’s Benjamin Good and his group tested this idea on 636 of the shared species. The work was delicate. Microbes evolve quickly. They also exchange their DNA with other strains, a process called horizontal gene transfer. This exchange blurs the family trees. Good’s team looked for several independent genetic signs to separate deeply shared ancestry from recent exchanges. They also tracked hereditary DNA mutations, which accumulate at a constant rate like clockwork, to estimate when species divide.
The results correspond to the history of humanity. The distribution periods for many species corresponded to migration out of Africa and subsequent movement to the Americas. Lead author Justin Sonnenburg, a microbiologist at Stanford, said the results show that these microbes traveled with people around the world and were passed from parent to child for thousands of years.
The gut microbiome digests fibrous foods, makes vitamins and trains the immune system. People in industrialized countries have much less microbial diversity. They also face more autoimmune diseases, type 2 diabetes and obesity. These conditions are rare in non-industrialized groups. The new study cannot prove that shedding causes the disease. This effectively shows that industrial life has erased the species that humans have preserved for tens of thousands of years, and this in just a few generations. Antibiotics, processed diets low in fiber and high in fat and sugar, and highly disinfected homes all play a role.
The consequences of this loss on human health are not yet clear. Researchers say that’s the next big question.
The risk is not limited to city dwellers. Food and access to medicines are changing rapidly in Tsimané communities. Gurven warns that their microbiomes may soon lose diversity and that this loss could harm their immunity and health.
Gn Health
