Article (Scientific journals)
Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota
Magnusdottir, Stefania; Heinken, Almut Katrin; Kutt, Laura et al.
2016In Nature Biotechnology
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Abstract :
[en] Genome-scale metabolic models derived from human gut metagenomic data can be used as a framework to elucidate how microbial communities modulate human metabolism and health. We present AGORA (assembly of gut organisms through reconstruction and analysis), a resource of genome-scale metabolic reconstructions semi-automatically generated for 773 human gut bacteria. Using this resource, we identified a defined growth medium for Bacteroides caccae ATCC 34185. We also showed that interactions among modeled species depend on both the metabolic potential of each species and the nutrients available. AGORA reconstructions can integrate either metagenomic or 16S rRNA sequencing data sets to infer the metabolic diversity of microbial communities. AGORA reconstructions could provide a starting point for the generation of high-quality, manually curated metabolic reconstructions. AGORA is fully compatible with Recon 2, a comprehensive metabolic reconstruction of human metabolism, which will facilitate studies of host–microbiome interactions.
Research center :
Luxembourg Centre for Systems Biomedicine (LCSB)
Disciplines :
Life sciences: Multidisciplinary, general & others
Author, co-author :
Magnusdottir, Stefania ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Heinken, Almut Katrin ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Kutt, Laura;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Ravcheev, Dmitry ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Bauer, Eugen ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Noronha, Alberto ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Greenhalgh, Kacy ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Jäger, Christian  ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Baginska, Joanna ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Wilmes, Paul ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Fleming, Ronan MT ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Thiele, Ines ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
External co-authors :
no
Language :
English
Title :
Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota
Publication date :
November 2016
Journal title :
Nature Biotechnology
ISSN :
1546-1696
Publisher :
Nature Publishing Group, New York, United States - New York
Peer reviewed :
Peer Reviewed verified by ORBi
Focus Area :
Systems Biomedicine
Available on ORBilu :
since 29 November 2016

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