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Metabolic Modeling of Human Gut Microbiota on a Genome Scale: An Overview
Örebro University, School of Medical Sciences. Örebro University Hospital. Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland; .ORCID iD: 0000-0003-0475-2763
Örebro University, School of Medical Sciences. Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland.ORCID iD: 0000-0002-2856-9165
2019 (English)In: Metabolites, ISSN 2218-1989, E-ISSN 2218-1989, Vol. 9, no 2, article id E22Article, review/survey (Refereed) Published
Abstract [en]

There is growing interest in the metabolic interplay between the gut microbiome and host metabolism. Taxonomic and functional profiling of the gut microbiome by next-generation sequencing (NGS) has unveiled substantial richness and diversity. However, the mechanisms underlying interactions between diet, gut microbiome and host metabolism are still poorly understood. Genome-scale metabolic modeling (GSMM) is an emerging approach that has been increasingly applied to infer diet⁻microbiome, microbe⁻microbe and host⁻microbe interactions under physiological conditions. GSMM can, for example, be applied to estimate the metabolic capabilities of microbes in the gut. Here, we discuss how meta-omics datasets such as shotgun metagenomics, can be processed and integrated to develop large-scale, condition-specific, personalized microbiota models in healthy and disease states. Furthermore, we summarize various tools and resources available for metagenomic data processing and GSMM, highlighting the experimental approaches needed to validate the model predictions.

Place, publisher, year, edition, pages
MDPI, 2019. Vol. 9, no 2, article id E22
Keywords [en]
Constraint-based modeling, flux balance, genome-scale metabolic modeling, gut microbiome, host–microbiome, meta-omics, metabolic reconstructions, metabolism, metabolomics, metagenomics
National Category
Bioinformatics (Computational Biology)
Identifiers
URN: urn:nbn:se:oru:diva-72041DOI: 10.3390/metabo9020022ISI: 000460288400006PubMedID: 30695998OAI: oai:DiVA.org:oru-72041DiVA, id: diva2:1288014
Note

Funding Agencies:

Academy of Finland (Centre of Excellence in Molecular Systems Immunology and Physiology Research)  250114 

Juvenile Diabetes Research Foundation  2-SRA-2014-159-Q-R 

European Union  634413 

Available from: 2019-02-12 Created: 2019-02-12 Last updated: 2019-06-18Bibliographically approved

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Sen, ParthoOresic, Matej

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