A generalizable approach is used to identify fitness determinants for multiple bacterial strains simultaneously in a model human gut microbiota, obtain gene-level characterization of their niches and responses to diet change, and design prebiotics for precision microbiota manipulation.. Fitness and diet responsiveness simultaneously defined in multiple Bacteroides strains in vivo

Defining the mechanisms critical for maintaining the highly adaptive and durable relationship between the human gut microbiota and its host is necessary if we are to understand how this community contributes to our health status, and how it can be manipulated to promote wellness. To help address this challenge, we generated libraries of tens of thousands of transposon (Tn) mutants for each of four human gut Bacteroides strains, two of which represented the same species. These libraries were introduced into singly-caged adult germ-free mice as part of a 15-member artificial human gut microbiota containing 11 other wild-type bacterial species. Mice received one of two distinct diets, or an ordered sequence of both. Multi-taxon INsertion Sequencing (INSeq) provided (i) a digital readout of the remarkably consistent pattern of community assembly, (ii) identified shared as well as species-, strain-, and diet-specific fitness determinants associated with a variety of metabolic/nutrient processing pathways, including those involving amino acids, carbohydrates and vitamins/cofactors, (iii) enabled quantitative gene-level measurement of the resiliency of the responses to diet perturbations, (iv) revealed that arabinoxylan, the most common hemicellulose in cereals, could be used to deliberately manipulate the representation of a prominent community member, Bacteroides cellulosilyticus WH2, and (v) defined the niche adjustments of this and the other Bacteroides to arabinoxylan supplementation of a high fat diet. The approach described for mapping microbial fitness landscapes in multiple strains simultaneously in a given community context should facilitate discovery efforts aimed at identifying the niches of microbiota members, as well as ways to deliberately reshape community structure and function through dietary interventions.