Even minimal exposure to modern medicine can rapidly change the human microbiome. In a new study publishing May 20 in the Cell Press journal Cell Reports, researchers reveal that the gut microbes of remote Amazonian Indigenous communities began shifting toward patterns more commonly seen in urban, industrialized populations after only a few medical visits.
"The study gives us a better idea of how sensitive human gut microbes are," says corresponding author Maria G. Dominguez-Bello of Rutgers University in New Jersey. "It opens the door for future research on how we can restore our microbiota after using medicines like antibiotics, which can deplete organisms in our gut."
Previous studies have shown that urbanization, including changes in diets, lifestyles, and living environments, can influence human gut microbes. But because these changes often happen at the same time, it is difficult for scientists to isolate each factor's impact on microbes.
Living in remote Amazonian jungles, Indigenous communities in Venezuela use ancestral knowledge and technology to fish, hunt, gather, and garden. Their traditional lifestyles and diets have remained largely unchanged over time. However, since late 2015, some villages have started receiving quarterly medical visits through a World Health Organization-supported program to treat and prevent onchocerciasis, or river blindness—a parasitic infection endemic to countries in Africa and Latin America. Through the program, the villagers receive routine antiparasitic medicine and basic medical care.
"The program offered a rare natural experiment," Dominguez-Bello says. "We know from studies in urban societies that antibiotics can have huge impacts on gut microbes," she says. "But we didn't know how even basic medicine might affect people with very limited exposure to medicine."
The research team visited the villages alongside the medical teams for the first time in October 2015 and again in February 2016. They collected samples from the gut, mouth, nose, and skin of 335 participants.
The team found the villagers' gut microbiota began to resemble that of people living in industrialized societies after the first medical visit, even without major changes in diet or lifestyle. Over four months of treatment, the villagers' gut microbial diversity declined, and the populations of Prevotella and Treponema—bacteria often associated with fiber digestion—diminished. At the same time, bacterial groups like Bacteroidota and Verrucomicrobia that are more common in industrialized populations became more abundant in the villagers.
The shifts are in line with the changes seen in a village with longer-term medical contact, where certain microbial groups have become progressively less common. These changes suggest that medical exposure may help drive the microbiome toward a more urbanized configuration, with the strongest shifts seen in children.
The team also analyzed how microbial function might have changed in the villagers. They found that after treatment, microbial genes involved in breaking down simple carbohydrates and developing antimicrobial resistance became more common in the gut, while genes linked to certain metabolic processes and fiber fermentation declined.
"The people living in these villages have almost twice the gut microbial diversity, and high diversity means they have multiple microbes performing similar functions," says Dominguez-Bello. "There is still a big difference between the microbiome of these communities and the average person in the United States. But if diversity continues to decline, there could be risks of losing important functions."
The changes were not limited to the gut. Researchers also found shifts in microbial communities in the mouth, nose, and on the skin, though each body site responded differently. For example, the villagers' oral microbial diversity declined, but nasal communities showed increased diversity after the first medical visit.
Dominguez-Bello says that programs treating infectious diseases such as river blindness provide lifesaving benefits, but future public health strategies could also consider ways to minimize impact on gut microbiome.
"Our findings suggest the microbiome is very sensitive and can change quickly," Dominguez-Bello says. "Many conditions, from obesity to allergies and even some cancers, are linked to gut microbes. Understanding how to protect and restore microbial diversity could become an important part of improving our health."
