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Nat Commun. 2017 Jun 6;8:15393. doi: 10.1038/ncomms15393.

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

Sung J1,2,3, Kim S1,4,5, Cabatbat JJT1, Jang S6, Jin YS7,8, Jung GY6,9, Chia N10,11,12, Kim PJ1,4,13.

Author information

1
Asia Pacific Center for Theoretical Physics, Pohang, Gyeongbuk 37673, Republic of Korea.
2
Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA.
3
Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
4
Department of Physics, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea.
5
The Abdus Salam International Centre for Theoretical Physics, 34151 Trieste, Italy.
6
Department of Chemical Engineering, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea.
7
Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
8
Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
9
School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea.
10
Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA.
11
Department of Surgery, Mayo Clinic, Rochester, Minnesota 55905, USA.
12
Department of Biomedical Engineering, Mayo College, Rochester, Minnesota 55905, USA.
13
Department of Physics, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.

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.

PMID:
28585563
PMCID:
PMC5467172
DOI:
10.1038/ncomms15393
[Indexed for MEDLINE]
Free PMC Article

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