Ecological succession in the human gut occurs over the first three years of life, as infants acquire and cultivate gut microbiota that play critical roles in modulating our health and digestion. Despite our familiarity with the general patterns of gut community succession, our understanding of the mechanisms that drive these patterns remains limited. In particular, it is unclear the degree to which gut succession is constrained by dispersal limitation relative to host development and/or host environment. Here, we use a custom trait database, drawn from several sources of publicly available phenotypic and genomic data, and a well resolved time-series of gut microbiome succession in 94 infants, to characterize trait-based changes in the gut microbiome over the first three years of human infant development. Unlike prior studies of gut microbiome succession, we expand the number of traits considered, characterize the changes quantitatively, and compare trait-based vs. taxonomic successional patterns to explore the relationship between community composition and community function.
Results/Conclusions
Early-arriving taxa included those with traits promoting short-distance dispersal and the ability to grow in stressful environments, which were gradually displaced by taxa better suited for the anaerobic gut environment and long-distance transmission among potential hosts. Intriguingly, trait-based successional patterns differed between infants born vaginally or by Cesarean section. Whereas most trait-based changes occurred over the first year of infant development, OTU-based changes continued steadily over the second and third years of development, underscoring the fact that taxonomic change does not necessarily imply functional changes (i.e., turnover can be functionally redundant). Lastly, we saw convergence in trait-based and OTU-based composition within and among infants over time, consistent with a deterministic community assembly process potentially limited by dispersal, rather than one dominated by historical contingencies or strong host differences.