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 interactions (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 a challenging 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.

Keywords: Dietary compositions; Gut microbiome; Inter-species relationships; Metabolic interactions; Metabolic simulations; Symbiotic relationships.

Graphical abstract

Fig. 1

Production and consumption of key metabolites simulated co-culturing of Bacteroides thetaiotaomicron (BT) and Methanobrevibacter smithii (MS) in 13 different diets(fluxes presented in mmol/gDW/hr units). Positive flux indicates metabolite production and negative flux indicates metabolite consumption. Diets marked in green (x-axis labels) indicate cases where the growth rate of MS increased by >10% in co-culturing with BT over its mono-culture growth. Diets marked in pink (x-axis labels) indicate cases where the growth rate of MS reduced by >10%.

Fig. 2

Schematic representation of the process followed for determining pairwise metabolic relationship between gut microbial species. The ‘>’ and ‘<’ symbols denote that the growth of an organism in paired simulations [G_org]^P (mimicking co-cultures) deviates at least by 10% or more when compared to its growth when simulated independently [G_org]^I (mimicking monoculture).