Journal
CURRENT OPINION IN SYSTEMS BIOLOGY
Volume 27, Issue -, Pages -Publisher
ELSEVIER
DOI: 10.1016/j.coisb.2021.05.007
Keywords
Constraint-based modelling; Microbe-microbe interactions; Host-microbe interactions; Microbiome; Gut; Human; Soil
Funding
- European Research Council (ERC) under the European Union [757922]
- National Institute on Aging [1RF1AG058942-01, 1U19AG063744-01]
- EMBO short-term fellowship [8720]
- European Research Council (ERC) [757922] Funding Source: European Research Council (ERC)
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This article provides a comprehensive overview of the applications of microbial multispecies models at the microbiome scale and the role of computational modeling in discovering novel biological knowledge. Constraint-based microbiome modeling complements experimental approaches and has valuable applications in ecology, human health, industry, and environmental conservation.
Microbial communities are near universally present in nature. A wealth of meta-omics data has been gathered from numerous ecosystems, such as the human gut, ocean or soil. Constraint-based reconstruction and analysis is a valuable tool for the contextualisation of meta-omics data and allows for the mechanistic prediction of metabolic fluxes. Advances in genome-scale reconstruction and multispecies modelling tools have enabled the construction and interrogation of constraint-based multispecies models on the microbiome scale spanning hundreds of organisms. Here, we give a comprehensive overview of the areas of application for these multiscale, strain- and molecule-resolved multispecies models, and discuss key works, in which computational modelling yielded novel biological knowledge. We show that constraint-based microbiome modelling can complement experimental approaches and has valuable applications spanning from ecology, human health, industry to environmental conservation.
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