Large-scale metabolic interaction network of the mouse and human gut microbiota

The role of our gut microbiota in health and disease is largely attributed
to the collective metabolic activities of the inhabitant microbes. A
system-level framework of the microbial community structure, mediated
through metabolite transport, would provide important insights into the
complex microbe-microbe and host-microbe chemical interactions. This
framework, if adaptable to both mouse and human systems, would be useful
for mechanistic interpretations of the vast amounts of experimental data
from gut microbiomes in murine animal models, whether humanized or not.
Here, we constructed a literature-curated, interspecies network of the
mammalian gut microbiota for mouse and human hosts, called NJC19. This
network is an extensive data resource, encompassing 838 microbial species
(766 bacteria, 53 archaea, and 19 eukaryotes) and 6 host cell types,
interacting through 8,224 small-molecule transport and macromolecule
degradation events. Moreover, we compiled 912 negative associations
between organisms and metabolic compounds that are not transportable or
degradable by those organisms. Our network may facilitate experimental and
computational endeavors for the mechanistic investigations of
host-associated microbial communities.