Reference : A functional metabolic map of Faecalibacterium prausnitzii, a beneficial human gut microbe

	Document type :	Scientific journals : Article
	Discipline(s) :	Life sciences : Multidisciplinary, general & others
	To cite this reference:	http://hdl.handle.net/10993/17459

Title :	A functional metabolic map of Faecalibacterium prausnitzii, a beneficial human gut microbe
Language :	English
Author, co-author :	Heinken, Almut Katrin [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 [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > > ; University of Iceland > Center for Systems Biology]
Publication date :	Sep-2014
Journal title :	Journal of Bacteriology
Publisher :	American Society for Microbiology (ASM)
Volume :	196
Issue/season :	18
Pages :	3289-3302
Peer reviewed :	Yes (verified by ORBilu)
Audience :	International
ISSN :	0021-9193
e-ISSN :	1098-5530
City :	Washington
Country :	DC
Abstract :	[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.
Research centres :	Luxembourg Centre for Systems Biomedicine (LCSB): Molecular Systems Physiology (Thiele Group)
Permalink :	http://hdl.handle.net/10993/17459
DOI :	10.1128/JB.01780-14
Other URL :	http://jb.asm.org/content/196/18/3289.long

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	Fulltext file(s): File Commentary Version Size Access Limited access 2014 - Heinken-Functional Metabolic Map of Faecalibacterium prausnitzii, a Beneficial Human Gut Microbe.pdf Publisher postprint 2.54 MB Request a copy Additional material(s): File Commentary Size Access Limited access 2014 - Heinken-Functional Metabolic Map of Faecalibacterium prausnitzii, a Beneficial Human Gut Microbe_SI.pdf 1.66 MB Request a copy

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