A compendium of predicted growths and derived symbiotic relationships between 803 gut microbes in 13 different diets

Abstract

Gut health is intimately linked to dietary habits and the microbial community (microbiota) that flourishes within. The delicate dependency of the latter on nutritional availability is also strongly influenced by symbiotic relationships (such as, parasitic or mutualistic) between the resident microbes, often affecting their growth rate and ability to produce key metabolites. Since, cultivating the entire repertoire of gut microbes is an infeasible task, metabolic models (genome-based metabolic reconstructions) could be employed to predict their growth patterns and interactions. Here, we have used 803 gut microbial metabolic models from the Virtual Metabolic Human repository, and subsequently optimized and simulated them to grow on 13 dietary compositions. The presented pairwise interaction data (https://osf.io/ay8bq/) and the associated bacterial growth rates are expected to be useful for (a) deducing microbial association patterns, (b) diet-based inference of personalised gut profiles, and (c) as a steppingstone for studying multi-species metabolic interactions.