Identifying determinants of bacterial fitness in a model of human gut microbial succession

Significance Postnatal development of the human gut microbiota is linked to healthy growth. Because the number of potential interactions between community components is vast, an unanswered question is what mechanisms determine the form of community assembly (succession). We created a simplified, manipulable in vivo model where bacterial strains cultured from an infant were divided into consortia, representing earlier and later periods in assembly, and introduced in different order into germ-free mice fed infant formula. Measuring strain abundances, bacterial gene expression and levels of gut nutrients, and applying computational tools to deduce interacting features, we identify genomic and metabolic correlates of how strains establish and maintain themselves. This approach may facilitate discoveries of how communities respond to various perturbations and microbiota-directed therapeutics. Human gut microbiota development has been associated with healthy growth but understanding the determinants of community assembly and composition is a formidable challenge. We cultured bacteria from serially collected fecal samples from a healthy infant; 34 sequenced strains containing 103,102 genes were divided into two consortia representing earlier and later stages in community assembly during the first six postnatal months. The two consortia were introduced alone (singly), or sequentially in different order, or simultaneously into young germ-free mice fed human infant formula. The pattern of fitness of bacterial strains observed across the different colonization conditions indicated that later-phase strains substantially outcompete earlier-phase strains, although four early-phase members persist. Persistence was not determined by order of introduction, suggesting that priority effects are not prominent in this model. To characterize succession in the context of the metabolic potential of consortium members, we performed in silico reconstructions of metabolic pathways involved in carbohydrate utilization and amino acid and B-vitamin biosynthesis, then quantified the fitness (abundance) of strains in serially collected fecal samples and their transcriptional responses to different histories of colonization. Applying feature-reduction methods disclosed a set of metabolic pathways whose presence and/or expression correlates with strain fitness and that enable early-stage colonizers to survive during introduction of later colonizers. The approach described can be used to test the magnitude of the contribution of identified metabolic pathways to fitness in different community contexts, study various ecological processes thought to govern community assembly, and facilitate development of microbiota-directed therapeutics.