Changes in the gut microbiota of urban subjects during an immersion in the traditional diet and lifestyle of a rainforest village

People living traditional lifestyles have higher gut microbiota diversity than urban subjects. We hypothesized that shifting lifestyles from an urban to a traditional rainforest village would lead to changes in the microbiota of visitors that would become more similar to the microbiota of villagers. Here, we characterized at different time points, the microbiota of 7 urban visitors (5 adults and 2 children) staying in a rainforest Amerindian village for 16 days, and compared them with reference collection of samples from age-matched local villagers. We performed a 16S rRNA gene survey in multiple body sites (fecal, oral, nasal and skin) using Illumina MiSeq sequencing. The main factor segregating the microbiotas of each body site was human group (i.e. visitors vs. villagers), with the visitor microbiota tending to have lower alpha diversity; the lowered alpha diversity was statistically significant in the microbiota of skin, and in the children’s fecal and oral microbiota. During the rainforest period, all visitors experienced microbiota changes within their personal cloud of variation. For all body sites, the microbiota conformations in visitor children better matched those in villagers of the same age, than did the microbiota of visitor adults, which showed lower “microbiota age” as compared to villagers. The results suggest a higher stability in the adult microbiota, with the less resilient children’s microbiota responding more to dietary changes.