Global metabolic interaction network of the human gut microbiota for context-specific community-scale analysis

TL;DR

This paper introduces NJS16, a comprehensive interspecies metabolic network of the human gut microbiota, enabling context-specific analysis of microbial communities and their metabolic functions in health and disease.

Contribution

It provides a curated, large-scale metabolic interaction network and a mathematical framework for analyzing gut microbiota in different health contexts, such as diabetes.

Findings

Identified core microbial entities with significant metabolic influence

Revealed disease-specific microbial and metabolic features in type 2 diabetes

Mapped community-wide metabolic interactions in the human gut

Abstract

A system-level framework of complex microbe-microbe and host-microbe chemical cross-talk would help elucidate the role of our gut microbiota in health and disease. Here we report a literature-curated interspecies network of the human gut microbiota, called NJS16. This is an extensive data resource composed of ~570 microbial species and 3 human cell types metabolically interacting through >4,400 small-molecule transport and macromolecule degradation events. Based on the contents of our network, we develop a mathematical approach to elucidate representative microbial and metabolic features of the gut microbial community in a given population, such as a disease cohort. Applying this strategy to microbiome data from type 2 diabetes patients reveals a context-specific infrastructure of the gut microbial ecosystem, core microbial entities with large metabolic influence, and frequently-produced metabolic compounds that might indicate relevant community metabolic processes. Our network presents a foundation towards integrative investigations of community-scale microbial activities within the human gut.