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Critical Reviews™ in Biomedical Engineering
SJR: 0.207 SNIP: 0.376 CiteScore™: 0.79

ISSN Print: 0278-940X
ISSN Online: 1943-619X

Critical Reviews™ in Biomedical Engineering

DOI: 10.1615/CritRevBiomedEng.2017024461
pages 459-472

The Virtual Microbiome: Computational Approaches to the Study of Microbe-Host Interactions

Joshua J. Pothen
Department of Medicine, University of Vermont College of Medicine, Burlington, VT 05405
Anne E. Dixon
Department of Medicine, University of Vermont College of Medicine, Burlington, VT 05405
Jason H. T. Bates
Department of Medicine, University of Vermont College of Medicine, Burlington, VT 05405


The GI tract of a normal adult human contains on the order of 1014 foreign living organisms, collectively known as the gut microbiome, the proper maintenance of which is critical for health. Because the gut microbiome is a dynamic system of vast complexity, computational modeling is assuming an increasingly important role in helping us to understand how and why it behaves as it does. In particular, computational models can serve as a rapid, cost-effective means of simulating the microbiome on multiple scales, from that of an individual bacterium to the microbiome as a whole. This not only allows questions to be addressed in ways that are impractical in the experimental laboratory; it also permits competing hypotheses to be interrogated for feasibility before they are subjected to expensive and time-consuming experimental testing. Here we review some of the differential equation–based and agent-based approaches that have been applied to the computational modeling of the gut microbiome and its effects on the rest of the body. The models discussed are helping us understand how the microbiome works as a system, how it maintains its crucial symbiotic relationship with its host, and, in particular, how its malfunctions can lead to a number of important and often serious pathologies.

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