Rapid microbiome restructuring associated with medical exposure in remote Amazonian Indigenous communities

Many factors contribute to reduced microbial diversity associated with Westernization, complicating efforts to identify early drivers of microbiome change. Here, we examine microbiome variation during the introduction of a sustained medical program into previously low-exposure remote Indigenous villages. We analyze fecal samples and body-site swabs from 335 Amerindians across multiple villages before and during repeated program visits, prior to major dietary or lifestyle transitions. Low-exposure villages show higher baseline gut microbiota diversity than the medium-exposure village, and microbiota diversity declines over time in association with repeated exposure, particularly in children. Changes include loss of specific gut taxa, reduced bacterial network connectivity, and shifts in functional gene profiles toward those reported in urban populations. Oral microbiota diversity decreases, while skin and nasal diversity show modest changes. These findings indicate that repeated exposure to basic medical interventions coincides with rapid microbiome restructuring during early stages of ecological transition.