Repeated exposure to basic medical interventions coincides with rapid microbiome restructuring during early stages of ecological transition in remote Amazonian Indigenous communities.
Key Findings
Results
Low-exposure villages showed higher baseline gut microbiota diversity than a medium-exposure village.
Study analyzed fecal samples and body-site swabs from 335 Amerindians across multiple villages
Villages were categorized by level of prior Western/medical exposure at baseline
Baseline gut microbiota diversity differences were observed before major dietary or lifestyle transitions had occurred
This finding suggests that exposure history, even prior to dietary change, correlates with microbiome diversity
Results
Gut microbiota diversity declined over time in association with repeated medical program exposure, particularly in children.
Samples were collected before and during repeated program visits from the same villages
The medical program represented a sustained introduction into previously low-exposure remote Indigenous villages
Children showed a stronger association between repeated exposure and diversity decline compared to adults
Changes occurred prior to major dietary or lifestyle transitions, isolating medical exposure as a correlate
Results
Repeated medical exposure was associated with loss of specific gut taxa and reduced bacterial network connectivity.
Specific gut taxa were lost over the course of repeated program visits
Bacterial network connectivity decreased, indicating disruption of microbial community structure beyond simple diversity metrics
These changes were observed in the context of remote villages with otherwise limited Western influence
The combination of taxon loss and reduced network connectivity suggests community-level restructuring
Results
Functional gene profiles of gut microbiota shifted toward those reported in urban populations following repeated medical exposure.
Metagenomic functional gene profiles were assessed in addition to taxonomic composition
Shifts in functional gene profiles were directionally consistent with profiles previously reported in urban/Westernized populations
These functional changes occurred during early stages of ecological transition, before major lifestyle changes
This indicates that microbiome functional capacity was altered alongside taxonomic changes
Results
Oral microbiota diversity decreased with repeated medical exposure, while skin and nasal microbiota showed only modest changes.
Multiple body sites were sampled including fecal, oral, skin, and nasal swabs
Oral microbiota exhibited decreases in diversity similar in direction to gut microbiota
Skin and nasal microbiota diversity changes were described as 'modest' compared to gut and oral sites
The differential responses across body sites suggest site-specific sensitivity to medical/Western exposure
Methods
The study design isolated medical program introduction as an early driver of microbiome change by sampling before major dietary or lifestyle transitions.
335 Amerindians were analyzed across multiple villages with varying levels of prior exposure
Sampling occurred before and during repeated medical program visits, controlling for timing of other Westernization factors
The remote setting and Indigenous population context allowed examination of microbiome change at a very early stage of ecological transition
Authors note that many factors contribute to reduced microbial diversity associated with Westernization, and this design aimed to identify early drivers
What This Means
This research examined how the gut and other microbiomes of remote Amazonian Indigenous people changed when a sustained medical program was introduced into their villages for the first time. By collecting samples from 335 people across multiple villages — before and during repeated medical visits, and before any major changes in diet or lifestyle — the researchers were able to track microbiome changes that coincided specifically with exposure to basic medical interventions rather than broader Westernization.
The study found that villages with less prior outside contact had more diverse gut microbiomes at the start, and that diversity declined over time as medical visits were repeated. This was especially pronounced in children. Beyond just diversity, specific bacterial species were lost, the connections between bacteria in the gut community became weaker, and the functional capabilities encoded by the microbial community shifted toward patterns seen in urban, Westernized populations. The mouth microbiome also showed diversity loss, while skin and nasal microbiomes changed less dramatically.
This research suggests that exposure to basic medical care — even before dietary or lifestyle changes take hold — may be an early driver of the microbiome shifts commonly observed when Indigenous or rural communities transition toward more Westernized ways of life. This matters because a less diverse microbiome has been associated with various health conditions in prior research. Understanding which specific exposures drive these early changes could inform efforts to preserve microbial diversity while still delivering necessary healthcare to underserved communities.
Sun H, Noya-Alarcon O, Wang J, Daniel S, Bittinger K, Mohamed W, et al.. (2026). Rapid microbiome restructuring associated with medical exposure in remote Amazonian Indigenous communities.. Cell reports. https://doi.org/10.1016/j.celrep.2026.117343