The human gut microbiome may be more sensitive to medical exposure than researchers once understood.
A new observational study published in Cell Reports found that gut microbes in remote Amazonian Indigenous communities began shifting toward patterns more often seen in industrialized populations after limited medical contact. The study does not show that modern medicine is harmful overall. Instead, it suggests that medicines and basic medical care may quickly affect the microbial communities that live in and on the body.
“The study gives us a better idea of how sensitive human gut microbes are,” said Maria G. Dominguez-Bello of Rutgers University, the study’s corresponding author. “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.”
Scientists already know that urbanization can affect the microbiome. Diet, sanitation, medication use, indoor living, processed foods and environmental exposures may all play a role. But because those changes often happen together, it can be difficult to separate one influence from another.
This study focused on Indigenous communities in the Venezuelan Amazon whose traditional foodways and lifestyles have remained largely distinct from those of industrialized populations. Since late 2015, some villages have received quarterly medical visits through a World Health Organization-supported program to treat and prevent onchocerciasis, also known as river blindness. The program provides routine antiparasitic medicine and basic medical care.
That setting gave researchers a rare opportunity to study how limited medical exposure may affect the microbiome without the same level of diet and lifestyle change often seen with urbanization.
The research team visited the villages with medical teams in October 2015 and again in February 2016. They collected samples from the gut, mouth, nose and skin of 335 participants.
After the first medical visits, the villagers’ gut microbes began to look more like those commonly seen in industrialized populations. Over four months, gut microbial diversity declined. Bacteria often associated with fiber digestion, including Prevotella and Treponema, became less common. At the same time, other bacterial groups more common in industrialized populations became more abundant.
The researchers also looked at what the microbes may be doing. After treatment, microbial genes involved in breaking down simple carbohydrates and developing antimicrobial resistance became more common in the gut. Genes linked to some 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,” Dominguez-Bello said. “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, although each area of the body responded differently.
The findings do not mean medical programs should be stopped. The treatments studied were part of an effort to prevent and treat river blindness, a serious parasitic disease that can damage vision and cause blindness. The study’s authors emphasized that such programs provide important health benefits.
The question, they suggest, is whether public health programs can eventually be designed to protect people from infectious disease while also paying closer attention to the microbiome.
“Our findings suggest the microbiome is very sensitive and can change quickly,” Dominguez-Bello said. “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.”
The study has several limits. It was observational, so it cannot prove that one medicine or one part of the medical visits caused every microbial change. It also focused on specific communities with very limited prior exposure to modern medicine, so the results should not be assumed to apply the same way to people living in industrialized settings.
The findings do, however, add to a larger body of research suggesting that the microbiome is shaped by much more than food alone. Diet matters, especially when it comes to fiber and the microbes that help break it down. But medications, infection control, sanitation, geography and environment may also influence which microbes thrive, decline or disappear.
This work was supported by the Canadian Institute for Advanced Research, the C&D Fund and the Emch Fund.