Towards Predictive Models of the Human Gut Microbiome

被引:75
作者
Bucci, Vanni [1 ]
Xavier, Joao B. [2 ]
机构
[1] Univ Massachusetts, Dept Biol, N Dartmouth, MA 02747 USA
[2] Mem Sloan Kettering Canc Ctr, Program Computat Biol, New York, NY 10065 USA
基金
美国国家卫生研究院;
关键词
mathematical modeling; network inference; metagenomics; antibiotic; biofilm; BIOLOGICAL PHOSPHORUS REMOVAL; 3-DIMENSIONAL COMPUTER-MODEL; WATER TREATMENT-PLANT; INTESTINAL MICROBIOTA; BACTERIAL; SYSTEMS; HETEROGENEITY; DOMINATION; DIVERSITY; EVOLUTION;
D O I
10.1016/j.jmb.2014.03.017
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
The intestinal microbiota is an ecosystem susceptible to external perturbations such as dietary changes and antibiotic therapies. Mathematical models of microbial communities could be of great value in the rational design of microbiota-tailoring diets and therapies. Here, we discuss how advances in another field, engineering of microbial communities for wastewater treatment bioreactors, could inspire development of mechanistic mathematical models of the gut microbiota. We review the state of the art in bioreactor modeling and current efforts in modeling the intestinal microbiota. Mathematical modeling could benefit greatly from the deluge of data emerging from metagenomic studies, but data-driven approaches such as network inference that aim to predict microbiome dynamics without explicit mechanistic knowledge seem better suited to model these data. Finally, we discuss how the integration of microbiome shotgun sequencing and metabolic modeling approaches such as flux balance analysis may fulfill the promise of a mechanistic model. (C) 2014 Elsevier Ltd. All rights reserved.
引用
收藏
页码:3907 / 3916
页数:10
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