Abstract
The human gut microbiome develops over early childhood and aids in food digestion and immunomodulation, but the mechanisms driving its development remain elusive. Here we use data curated from literature and online repositories to examine trait-based patterns of gut microbiome succession in 56 infants over their first three years of life. We also develop a new phylogeny-based approach of inferring trait values that can extend readily to other microbial systems and questions. Trait-based patterns suggest that infant gut succession begins with a functionally variable cohort of taxa, adept at proliferating rapidly within hosts, which gradually matures into a more functionally uniform cohort of taxa adapted to thrive in the anoxic gut and disperse between anoxic patches as oxygen-tolerant spores. Trait-based composition stabilizes after the first year, while taxonomic turnover continues unabated, suggesting functional redundancy in the traits examined. Trait-based approaches powerfully complement taxonomy-based approaches to understanding the mechanisms of microbial community assembly and succession.
Highlights
The human gut microbiome develops over early childhood and aids in food digestion and immunomodulation, but the mechanisms driving its development remain elusive
With respect to taxonomic composition, early succession was dominated by Bacteroidaceae and Bifidobacteriaceae (Fig. 1a, b), whereas late succession was dominated by Lachnospiraceae, Ruminococcaceae, and Bacteroidaceae (Fig. 1e,f)
The stabilization of trait-based community composition after the first year of development (Fig. 4), and the drop in variance of predicted trait values in gut communities for most traits over time (Supplementary Figure 4), both suggest that succession is at least partially functionally deterministic, with early dynamics potentially reflecting stochastic colonization during the birthing process, followed by the gradual colonization and enrichment of a more functionally uniform cohort of taxa better adapted for the mature gut environment
Summary
The human gut microbiome develops over early childhood and aids in food digestion and immunomodulation, but the mechanisms driving its development remain elusive. Despite the success and proliferation of trait-based approaches to study community assembly in plant[17,18], animal[19,20], and phytoplankton systems[21], they have only rarely been used for bacterial and archaeal systems[22,23]. This is due partly to the challenges of identifying ecologically relevant traits for a functionally diverse cohort of taxa, and partly to a dearth of curated trait data. Thanks to recent advances in high-throughput molecular techniques, renewed efforts to directly collect phenotypic data[24], and the aggregation of data from disparate sources[25,26], trait-based approaches to microbial community dynamics are becoming more feasible, especially for well-studied systems like the human gut
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