Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Review
. 2021 Jun 14;17(3):365-375.
doi: 10.1039/d0mo00154f.

Mechanistic models of microbial community metabolism

Lillian R Dillard  1 , Dawson D Payne, Jason A Papin
Affiliations
Review

Mechanistic models of microbial community metabolism

Lillian R Dillard et al. Mol Omics. .

Abstract

Microbial communities affect many facets of human health and well-being. Naturally occurring bacteria, whether in nature or the human body, rarely exist in isolation. A deeper understanding of the metabolic functions of these communities is now possible with emerging computational models. In this review, we summarize frameworks for constructing mechanistic models of microbial community metabolism and discuss available algorithms for model analysis. We highlight essential decision points that greatly influence algorithm selection, as well as model analysis. Polymicrobial metabolic models can be utilized to gain insights into host-pathogen interactions, bacterial engineering, and many more translational applications.

PubMed Disclaimer

Conflict of interest statement

There are no conflicts of interest to declare.

Figures

Fig. 1
Fig. 1. (a) Multi-omic data integration into GEMs during model construction, contextualization, validation and analysis. (b) How GEMs simulate the physiological conditions of an organism.
Fig. 2
Fig. 2. Essential decision points to consider during polymicrobial community model construction.
See this image and copyright information in PMC

References

    1. Krajmalnik-Brown R. Ilhan Z. E. Kang D. W. DiBaise J. K. Effects of gut microbes on nutrient absorption and energy regulation. Nutr. Clin. Pract. 2012;27(2):201–214. doi: 10.1177/0884533611436116. - DOI - PMC - PubMed
    1. Libertucci J. Young V. B. The role of the microbiota in infectious diseases. Nat. Microbiol. 2019;4(1):35–45. doi: 10.1038/s41564-018-0278-4. - DOI - PubMed
    1. Baeshen N. A. Baeshen M. N. Sheikh A. Bora R. S. Ahmed M. M. M. Ramadan H. A. Saini K. S. et al., Cell factories for insulin production. Microb. Cell Fact. 2014;13(1):1–9. doi: 10.1186/s12934-014-0141-0. - DOI - PMC - PubMed
    1. Vishwakarma K., Sharma S., Kumar N., Upadhyay N., Devi S. and Tiwari A., Contribution of microbial inoculants to soil carbon sequestration and sustainable agriculture, in Microbial inoculants in sustainable agricultural productivity, Springer, New Delhi, 2016, pp. 101–113
    1. Fang X. Lloyd C. J. Palsson B. O. Reconstructing organisms in silico: genome-scale models and their emerging applications. Nat. Rev. Microbiol. 2020;18(12):731–743. - PMC - PubMed

Publication types