The indigenous human gut microbiome is naturally resistant to colonization by exogenous bacteria. Severe perturbations to its ecosystem, such as antibiotics, can however result in loss of colonization resistance. Members of the indigenous and perturbed human gut have been associated with resistance against specific invaders. Yet, individual microbes do not always drive colonization resistance. Rather, multiple diverse assemblages can collectively mediate it. To probe the context-dependency of colonization resistance in the human gut, we developed a high-throughput in vitro experimental pipeline for identifying associations between gut community structure and ecosystem function. We generated a large library of human feces-derived microbial communities (microcosms) that vary by species richness and community membership. We incubated our microcosms in anoxic gut media for 48 hours and profiled their community composition with high-throughput sequencing of the 16S rRNA gene.
Our approach successfully constructed a library with high variation in taxonomic composition between microcosms, akin to the inter-individual variation between the gut microbiomes of a human cohort, and high variation in community productivity as measured by optical density. We then challenged our library with gfp-tagged Escherichia coli and observed high variation in the ability of communities to resist E. coli. Our approach also defined global patterns in the structure-function relationships of the human gut ecosystem. As a proof-of-concept, we observed positive correlation between community richness and productivity (Spearman’s rho=0.60, P<0.01), and between community richness and colonization resistance (Spearman’s rho=0.55, P<0.01). Our pipeline also enabled high-throughput measurements of additional community functions such as oxygen respiration, a phenotype previously associated with colonization resistance.
In summary, our approach can create a large library of microcosms, profile their microbial composition and emergent phenotypes. More importantly, it allows for high-throughput associations of community structure and colonization resistance. Therefore, our work will generate hypotheses on how microbial assemblages act in concert to mediate colonization resistance and inform strategies for engraftment of probiotics and resistance of pathogens in the human gut.