Modern Medicine Alters the Gut Microbiome, Study of Indigenous Amazonians Finds

Urbanization, which includes changes in lifestyle, diet, and environment, has been linked to alterations in the human gut microbiome. However, as these changes often occur simultaneously, it has been difficult for scientists to isolate the effects of individual factors.

A unique opportunity to study microbiome changes in remote Amazonian Indigenous communities has now shed light on how one such component of urbanization, modern medicine, can change the human microbiome. Published in the journal Cell Reports, the study showed that after only a few medical visits, the gut microbes of Indigenous communities began shifting towards patterns associated with westernization.

Gut microbial diversity declined over time with repeated exposure to medical interventions, particularly in children, which the researchers said underscores the importance of developing public health strategies that preserve the benefits of medicine while remaining conscious of any long-term impacts on the microbiome.

A rare chance to isolate the impacts of modern medicine on the gut

For the study, researchers sampled the microbiomes of 335 Indigenous people from multiple remote villages in Venezuela. These Indigenous communities use their ancestral knowledge and technology to fish, hunt, gather, and garden. Their lifestyle and diets have largely remained unchanged over time.

In 2015, the Carter Center’s Onchocerciasis Elimination Program for the Americas (OEPA)—a World Health Organization-supported program aimed at treating and preventing onchocerciasis—began conducting quarterly medical visits to the remote villages. As part of these visits, villagers received routine antiparasitic medicine and basic medical care. This presented a rare opportunity to study how basic medicine affects the gut microbiomes of people with very limited previous exposure.

“Remote Indigenous communities still preserve high microbial diversity, but as they are now increasingly exposed to modern medicine and globalization, we wanted to understand how rapidly the microbiome changes during these early stages of transition,” corresponding author Prof. Maria G. Dominguez-Bello of Rutgers University told Technology Networks.

The research team visited seven small, remote villages when they were integrated into the OEPA program, as well as one comparison village with longer-term exposure to Western visitors and medicine, where onchocerciasis is not endemic. Samples from the gut, mouth, nose, and skin were collected in October 2015 and February 2016 and analyzed using next-generation sequencing.

Modern medicine decreases gut microbial diversity

After the first medical visit, the researchers observed that the villagers’ gut microbiota began to resemble that of people living in industrialized societies. Over four months of treatment, the villagers’ gut microbial diversity declined, and members of the genera Prevotella and Treponema diminished. Bacterial taxa more common in industrialized populations, such as multiple Bacteroidota and Verrucomicrobia, became more abundant with increasing exposure. These shifts were in line with those observed for the comparison village.

“These findings are consistent with microbiome westernization, which is typically associated with reduced microbial diversity and loss of ancestral microbes,” said Dominguez-Bello. “What was striking was how rapidly these changes appeared, even in communities that still maintain largely traditional lifestyles.”

The researchers also analyzed changes in microbial function among the villagers. They observed that after treatment, pathways related to simple carbohydrate utilization and antimicrobial resistance were enriched. On the other hand, pathways linked to core biosynthetic and energy metabolism, and to fiber fermentation were reduced.

“Many fiber-fermenting microbes rely on plant-rich diets and stable transmission across generations, but they also seem especially vulnerable to environmental and medical disturbances,” Dominguez-Bello explained. “As these microbial communities are disrupted, important metabolic functions may disappear as well.”

Children exhibited the most pronounced microbiome changes across visits. “We think the stronger microbiome changes observed in children reflect the lower resilience of the developing microbiome,” stated Dominguez-Bello.

“Early life appears to represent a particularly sensitive biological window during which microbial perturbations may have long-lasting effects on health.” — Prof. Maria G. Dominguez-Bello.

This observation raises questions about how repeated medical visits during early childhood may impact long-term health trajectories, especially in populations undergoing societal transition, the researchers suggest.

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Beyond the gut, oral, nasal, and skin microbiomes also changed with exposure, although with site-specific patterns. Oral microbiota diversity declined with exposure, while nasal microbiota diversity increased across visits. Skin communities showed declining diversity and loss of multiple Actinobacteriota and Bacillota taxa.

Implications for future public health strategies

The findings of the study add to mounting evidence that microbiome westernization is a process that begins early and progresses incrementally. Decreases in gut microbial diversity suggest that even essential medical interventions may coincide with unintended consequences for the human microbiome. Understanding and navigating this balance is essential, the researchers said, especially for Indigenous communities in transition. Access to modern medical care may reduce infectious disease burden but could diminish microbial diversity.

Many conditions, such as obesity and even some cancers, have been linked to the gut microbiome. Dominguez-Bello believes that protecting microbial diversity could therefore become an important part of improving human health.

“These findings highlight the importance of developing restorative approaches for the microbiome to recover after disruption. We are not going to give up modern medicine. We need it. But we should also find ways to repair the collateral damage to the microbiome, especially in early age when the microbiome is maturing,” she concluded.

Reference: Sun H, Noya-Alarcon O, Wang J, et al. Rapid microbiome restructuring associated with medical exposure in remote Amazonian Indigenous communities. Cell Rep. 2026;45(5). doi: 10.1016/j.celrep.2026.117343

About the interviewee:

Dr. Maria Gloria Dominguez-Bello is a distinguished professor at Rutgers University in New Jersey. She received her PhD from the University of Aberdeen, Scotland. Her research focuses on the microbiome, including development from birth, functions for the host, impact by modern urban practices that reduce microbial transmission or disrupt the microbiota, and strategies for restoration.