Ecological modeling from metagenomics: predicting multi-species microbial dynamics relevant to Clostridium di fficile infection
The intestinal microbiota is a microbial ecosystem of crucial importance to human health. Understanding how the microbiota confers resistance against enteric pathogens and how antibiotics disrupt that resistance is key to the prevention and cure of intestinal infections. In this talk I will present recent work to infer microbiota ecology directly from time-resolved metagenomics and predict its temporal dynamics. Data from recent experiments on antibiotic-mediated Clostridium diffi cile infection are analyzed to quantify microbial interactions, commensal-pathogen interactions, and the effect of the antibiotic on the community. Numerical simulations and linear stability analysis confirm that the microbiota is multistable and that antibiotic perturbations and C. di fficile inoculation can produce catastrophic shifts that persist even after removal of the perturbations. Importantly, we identify a subnetwork of bacterial groups implicated in protection against C. diffi cile, which is common to mice as well as hospitalized cancer patients.