Emerging methods for genome-scale metabolic modeling of microbial communities

Trends Endocrinol Metab. 2024 Apr 3:S1043-2760(24)00062-6. doi: 10.1016/j.tem.2024.02.018. Online ahead of print.ABSTRACTGenome-scale metabolic models (GEMs) are consolidating as platforms for studying mixed microbial populations, by combining biological data and knowledge with mathematical rigor. However, deploying these models to answer research questions can be challenging due to the increasing number of available computational tools, the lack of universal standards, and their inherent limitations. Here, we present a comprehensive overview of foundational concepts for building and evaluating genome-scale models of microbial communities. We then compare tools in terms of requirements, capabilities, and applications. Next, we highlight the current pitfalls and open challenges to consider when adopting existing tools and developing new ones. Our compendium can be relevant for the expanding community of modelers, both at the entry and experienced levels.PMID:38575441 | DOI:10.1016/j.tem.2024.02.018

Source: Trends in Endocrinology and Metabolism: TEM - April 4, 2024 Category: Endocrinology Authors: Chaimaa Tarzi Guido Zampieri Neil Sullivan Claudio Angione Source Type: research