Metabolic Modeling of Human Gut Microbiota on a Genome Scale: An Overview

Sen, Partho,1983-Örebro universitet,Institutionen för medicinska vetenskaper,Region Örebro län,Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland; (author)

Metabolic Modeling of Human Gut Microbiota on a Genome Scale : An Overview

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
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.

Oresic, Matej,1967-Örebro universitet,Institutionen för medicinska vetenskaper,Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland(Swepub:oru)moc (author)
Örebro universitetInstitutionen för medicinska vetenskaper (creator_code:org_t)

About the subject

NATURAL SCIENCES: NATURAL SCIENCES; and Computer and Inf ...; and Bioinformatics

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