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

Authors
  • Sen, Partho1
  • Orešič, Matej1
  • 1 School of Medical Sciences, Örebro University, 702 81 Örebro, Sweden
Type
Published Article
Journal
Metabolites
Publisher
MDPI
Publication Date
Jan 28, 2019
Volume
9
Issue
2
Identifiers
DOI: 10.3390/metabo9020022
PMID: 30695998
PMCID: PMC6410263
Source
PubMed Central
Keywords
License
Green

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.

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