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Metabolites 2019, 9(2), 22; https://doi.org/10.3390/metabo9020022

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

1,2,* and 1,2
1
Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, FI-20520 Turku, Finland
2
School of Medical Sciences, Örebro University, 702 81 Örebro, Sweden
*
Author to whom correspondence should be addressed.
Received: 25 November 2018 / Revised: 23 January 2019 / Accepted: 24 January 2019 / Published: 28 January 2019
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Abstract

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. View Full-Text
Keywords: gut microbiome; meta-omics; metagenomics; metabolomics; metabolic reconstructions; genome-scale metabolic modeling; constraint-based modeling; flux balance; host–microbiome; metabolism gut microbiome; meta-omics; metagenomics; metabolomics; metabolic reconstructions; genome-scale metabolic modeling; constraint-based modeling; flux balance; host–microbiome; metabolism
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).
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Sen, P.; Orešič, M. Metabolic Modeling of Human Gut Microbiota on a Genome Scale: An Overview. Metabolites 2019, 9, 22.

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