Temporal dynamics of gut microbiomes in non-industrialized urban Amazonia

ABSTRACT Background Increasing levels of industrialization have been associated with changes in gut microbiome structure and loss of features thought to be crucial for maintaining gut ecological balance. The stability of gut microbial communities over time within individuals seems to be largely affected by this transition but has been overlooked among transitioning populations from low to middle-income countries. Here, we used shotgun sequencing to characterize the temporal dynamics of gut microbiomes of 24 individuals living in an urban non-industrialized lifestyle in the Brazilian Amazon and contextualized our data with 165 matching longitudinal samples from an urban industrialized and a rural non-industrialized population. Results We show that gut microbiome composition and diversity have greater variability over time among non-industrialized individuals when compared to industrialized counterparts and that taxa may present diverse temporal dynamics across human populations. Enterotype classifications show community types are generally stable over time despite shifts in microbiome structure. Further, by tracking genomes over time, we show that levels of bacterial population replacements are more frequent among Amazonian individuals and non-synonymous variants accumulate in genes associated with degradation of host dietary polysaccharides. Conclusions Our results suggest that the stability of gut microbiomes is influenced by levels of industrialization and that tracking microbial population dynamics is important to understand how the microbiome will adapt to these transitions.