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Ghim, Cheol-Min
Physical Biology & Biological Physics
Research Interests
  • Control of complex networks, Stochastic fluctuations in a cell, Biochemical information processing, Human microbiome, Ecological inference, Nonequilibrium active system

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

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Title
Large-scale metabolic interaction network of the mouse and human gut microbiota
Author
Lim, RoktaekCabatbat, Josephine Jill T.Martin, Thomas L. P.Kim, HaneulKim, SeunghyeonSung, JaeyunGhim, Cheol-MinKim, Pan-Jun
Issue Date
2020-06
Publisher
NATURE PUBLISHING GROUP
Citation
SCIENTIFIC DATA, v.7, no.1, pp.204
Abstract
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.
URI
https://scholarworks.unist.ac.kr/handle/201301/32319
URL
https://www.nature.com/articles/s41597-020-0516-5
DOI
10.1038/s41597-020-0516-5
ISSN
2052-4463
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