Advances in constraint-based modelling of microbial communities. Issue 27 (September 2021)

• Record Type: Journal Article
• Authors: Heinken, Almut; Basile, Arianna; Thiele, Ines
• Is Part Of: Current opinion in systems biology. Issue 27(2021)
• Publication Date: 2021-09
• Subjects: Constraint-based modelling -- Microbe-microbe interactions -- Host-microbe interactions -- Microbiome -- Gut -- Human -- Soil; Systems biology -- Periodicals; 570
• DOI: 10.1016/j.coisb.2021.05.007
• Languages: English
• ISSNs: 2452-3100

Abstract

Abstract: 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. Highlights: Constraint-based Reconstruction and Analysis (COBRA) is a mechanistic computational metabolic modelling approach. We provide a comprehensive survey of all studies to date that used COBRA modelling to interrogate microbiome interactions. The scope and size of COBRA modelling has increased in recent years due to advances in the field. COBRA microbiome modelling has been applied to a variety of areas from human health to industry and environmental research. Future applications will lead to mechanistic insight into diverse microbiomes, e.g., human gut, soil, or ocean.