From next-generation sequencing to systematic modeling of the gut microbiome
Review article, 2015
Changes in the human gut microbiome are associated with altered human metabolism and health, yet the mechanisms of interactions between microbial species and human metabolism have not been clearly elucidated. Next-generation sequencing has revolutionized the human gut microbiome research, but most current applications concentrate on studying the microbial diversity of communities and have at best provided associations between specific gut bacteria and human health. However, little is known about the inner metabolic mechanisms in the gut ecosystem. Here we review recent progress in modeling the metabolic interactions of gut microbiome, with special focus on the utilization of metabolic modeling to infer host-microbe interactions and microbial species interactions. The systematic modeling of metabolic interactions could provide a predictive understanding of gut microbiome, and pave the way to synthetic microbiota design and personalized-microbiome medicine and healthcare. Finally, we discuss the integration of metabolic modeling and gut microbiome engineering, which offer a new way to explore metabolic interactions across members of the gut microbiota.
Personalized medicine
Systematic modeling
Gut microbiome
microbial community
microbial metabolism
Next-generation sequencing
microbiome
Review
molecular interaction
Species interactome
methanogenesis
human
nonhuman
phenotype
intestine flora
next generation sequencing
model
metagenomics
Metabolic modeling
Author
Boyang Ji
Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology
Jens B Nielsen
Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology
Frontiers in Genetics
16648021 (eISSN)
Vol. 6 JUN 219Subject Categories
Biological Sciences
Areas of Advance
Life Science Engineering (2010-2018)
DOI
10.3389/fgene.2015.00219