  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.
