Reference : A functional metabolic map of Faecalibacterium prausnitzii, a beneficial human gut microbe
Scientific journals : Article
Life sciences : Multidisciplinary, general & others
http://hdl.handle.net/10993/17459
A functional metabolic map of Faecalibacterium prausnitzii, a beneficial human gut microbe
English
Heinken, Almut Katrin mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > > ; University of Iceland > Center for Systems Biology]
Khan, M Tanweer [University of Groningen, University Medical Center Groningen > Department of Medical Microbiology]
Paglia, Giuseppe [University of Iceland > Center for Systems Biology]
Rodionov, Dmitry A [Sanford-Burnham Medical Research Institute > > > ; A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences]
Harmsen, Hermie JM [University of Groningen, University Medical Center Groningen > Department of Medical Microbiology]
Thiele, Ines mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > > ; University of Iceland > Center for Systems Biology]
Sep-2014
Journal of Bacteriology
American Society for Microbiology (ASM)
196
18
3289-3302
Yes (verified by ORBilu)
International
0021-9193
1098-5530
Washington
DC
[en] The human gut microbiota plays a central role in human well-being and disease. In this study, we present an integrated, iterative approach of computational modeling, in vitro experiments, metabolomics, and genomic analysis to accelerate the identification of metabolic capabilities for poorly characterized (anaerobic) microorganisms. We demonstrate this approach for the beneficial human gut microbe Faecalibacterium prausnitzii strain A2-165. We generated an automated draft reconstruction, which we curated against the limited biochemical data. This reconstruction modeling was used to develop in silico and in vitro a chemically defined medium (CDM), which was validated experimentally. Subsequent metabolomic analysis of the spent medium for growth on CDM was performed. We refined our metabolic reconstruction according to in vitro observed metabolite consumption and secretion and propose improvements to the current genome annotation of F. prausnitzii A2-165. We then used the reconstruction to systematically characterize its metabolic properties. Novel carbon source utilization capabilities and inabilities were predicted based on metabolic modeling and validated experimentally. This study resulted in a functional metabolic map of F. prausnitzii, which is available for further applications. The presented workflow can be readily extended to other poorly characterized and uncharacterized organisms to yield novel biochemical insights about the target organism.
Luxembourg Centre for Systems Biomedicine (LCSB): Molecular Systems Physiology (Thiele Group)
http://hdl.handle.net/10993/17459
10.1128/JB.01780-14
http://jb.asm.org/content/196/18/3289.long

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