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

Jaeyun Sung; Seunghyeon Kim; Josephine Jill T. Cabatbat; Sungho Jang; Yong Su Jin; Gyoo Yeol Jung; Nicholas Chia; Pan Jun Kim

doi:10.1038/ncomms15393

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

Jaeyun Sung, Seunghyeon Kim, Josephine Jill T. Cabatbat, Sungho Jang, Yong Su Jin, Gyoo Yeol Jung, Nicholas Chia, Pan Jun Kim^*

^*Corresponding author for this work

Department of Biology

Research output: Contribution to journal › Journal article › peer-review

174 Citations (Scopus)

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.

Original language	English
Article number	15393
Number of pages	12
Journal	Nature Communications
Volume	8
DOIs	https://doi.org/10.1038/ncomms15393
Publication status	Published - 6 Jun 2017

Scopus Subject Areas

Chemistry(all)
Biochemistry, Genetics and Molecular Biology(all)
Physics and Astronomy(all)

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This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1038/ncomms15393

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

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.",

author = "Jaeyun Sung and Seunghyeon Kim and Cabatbat, {Josephine Jill T.} and Sungho Jang and Jin, {Yong Su} and Jung, {Gyoo Yeol} and Nicholas Chia and Kim, {Pan Jun}",

note = "Funding Information: We thank H. Bj{\o}rn Nielsen, Matthew Benedict, Matthew Gonnerman and Caroline B. M. Porter for useful discussions. This work was supported by the National Research Foundation of Korea (NRF) Grant NRF-2015R1C1A1A02037045 (J.S., S.K., J.J.T.C. and P.-J.K.) and NRF-2015R1A2A1A10056126 (S.J. and G.Y.J.), and the Advanced Biomass R&D Center (ABC) of Global Frontier Project ABC-2015M3A6A2066119 (S.J. and G.Y.J.) funded by the Korean Government (MSIP). This work was also supported by the ICTP through the OEA-AC-98 (S.K.), the Mayo Clinic Center for Individualized Medicine (N.C.) and the National Institutes of Health under award number R01CA179243 (N.C.). Publisher Copyright: {\textcopyright} The Author(s) 2017",

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AU - Sung, Jaeyun

AU - Kim, Seunghyeon

AU - Cabatbat, Josephine Jill T.

AU - Jang, Sungho

AU - Jin, Yong Su

AU - Jung, Gyoo Yeol

AU - Chia, Nicholas

AU - Kim, Pan Jun

N1 - Funding Information: We thank H. Bjørn Nielsen, Matthew Benedict, Matthew Gonnerman and Caroline B. M. Porter for useful discussions. This work was supported by the National Research Foundation of Korea (NRF) Grant NRF-2015R1C1A1A02037045 (J.S., S.K., J.J.T.C. and P.-J.K.) and NRF-2015R1A2A1A10056126 (S.J. and G.Y.J.), and the Advanced Biomass R&D Center (ABC) of Global Frontier Project ABC-2015M3A6A2066119 (S.J. and G.Y.J.) funded by the Korean Government (MSIP). This work was also supported by the ICTP through the OEA-AC-98 (S.K.), the Mayo Clinic Center for Individualized Medicine (N.C.) and the National Institutes of Health under award number R01CA179243 (N.C.). Publisher Copyright: © The Author(s) 2017

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AB - 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.

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

Abstract

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UN SDGs

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