Convergent temporal dynamics of the human infant gut microbiota

Abstract

Temporal dynamics of the human gut microbiota is of fundamental importance for the development of proper gut function and maturation of the immune system. Here we present a description of infant gut ecological dynamics using a combination of nonlinear data modeling and simulations of the early infant gut colonization processes. Principal component analysis of infant microbiota 16S rRNA gene microarray data showed that the main directions of variation were defined by three phylum-specific probes targeting Bacteroides, Proteobacteria and Firmicutes. Nonlinear regression analysis identified several dynamic interactions between these three phyla. Simulations of the early phylum-level colonization process showed the relatively rapid establishment of an equilibrium community after an unstable initial phase. In general, varying the initial composition of phyla in the simulations had little bearing on the final equilibrium. The dynamic interaction model was found to maintain its predictive ability for Proteobacteria and Firmicutes well into the simulation, whereas Bacteroides densities tended to be underestimated, possibly due to host top-down selection for Bacteroides. In accordance with our model, initial perturbation of the microbiota by different mode of delivery (vaginal and C-section) did not affect the later phylum composition in the infants investigated. Considering the predictive ability and convergence of our phylum-level model, we now propose that deterministic bacterial-bacterial interactions are more important for shaping the human infant gut microbiota than previously anticipated.

Strain-resolved community genomic analysis of gut microbial colonization in a premature infant

“…In infants, early assembly of the gut microbiota has been linked to development of innate immune responses and terminal differentiation of intestinal structures (4). The dynamic process of colonization has been well studied at high taxonomic levels (5) and seems predictable based on competitive interactions between and within the dominant phyla (6). Yet at lower taxonomic levels, and at early stages of development, our knowledge of this process is incomplete.…”

Community history affects the predictability of microbial ecosystem development

“…Importantly, our results show variability between replicate communities at the functional level (assessed in this study by redox potential) as well as at the taxon level. In our microcosms, as in environmental microbial communities (Trosvik et al, 2010;Burke et al, 2011), it is likely that the set of key microbial ecotypes that is present is reproducible across microcosms. However, our results suggest that variability at the taxon level can have a substantial effect on community function, even between replicate microcosms.…”

Phylogenetic Diversity of Diazotrophs along an Experimental Nutrient Gradient in Mangrove Sediments

“…Our study reports, for the first time, the application of GAM models to elucidate the microbial ecology of specific functional traits in mangrove sediments. These niche-based species distribution models [76] have been applied to a wide range of plants, macroorganisms and microorganisms [14,[77][78][79] and consist of observations of species over a gradient of environmental parameters (or "predictors") that can have a direct or indirect effect on the establishment or survival of the species at a limited time period. GAM models assume pseudo-equilibrium between the environmental parameters and the species spatial pattern underlying the realized niche for the species studied [76].…”