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Open AccessArticle

NetMet: A Network-Based Tool for Predicting Metabolic Capacities of Microbial Species and their Interactions

Institute of Plant Sciences, Newe Ya’ar Research Center, The Agricultural Research Organization, Ramat Yishay 30095, Israel
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Author to whom correspondence should be addressed.
These authors contributed equally as first authors.
Microorganisms 2020, 8(6), 840; https://doi.org/10.3390/microorganisms8060840
Received: 11 May 2020 / Revised: 1 June 2020 / Accepted: 2 June 2020 / Published: 3 June 2020
(This article belongs to the Special Issue Applying Metaorganism Studies to the Fruit Microbiome: A New Frontier)
Metabolic conversions allow organisms to produce a set of essential metabolites from the available nutrients in an environment, frequently requiring metabolic exchanges among co-inhabiting organisms. Genomic-based metabolic simulations are being increasingly applied for exploring metabolic capacities, considering different environments and different combinations of microorganisms. NetMet is a web-based tool and a software package for predicting the metabolic performances of microorganisms and their corresponding combinations in user-defined environments. The algorithm takes, as input, lists of (i) species-specific enzymatic reactions (EC numbers), and (ii) relevant metabolic environments. The algorithm generates, as output, lists of (i) compounds that individual species can produce in each given environment, and (ii) compounds that are predicted to be produced through complementary interactions. The tool is demonstrated in two case studies. First, we compared the metabolic capacities of different haplotypes of the obligatory fruit and vegetable pathogen Candidatus Liberibacter solanacearum to those of their culturable taxonomic relative Liberibacter crescens. Second, we demonstrated the potential production of complementary metabolites by pairwise combinations of co-occurring endosymbionts of the plant phloem-feeding whitefly Bemisia tabaci. View Full-Text
Keywords: metabolic networks; microbial interactions; genomics; environment; network modeling; expansion algorithm; simulation metabolic networks; microbial interactions; genomics; environment; network modeling; expansion algorithm; simulation
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Tal, O.; Selvaraj, G.; Medina, S.; Ofaim, S.; Freilich, S. NetMet: A Network-Based Tool for Predicting Metabolic Capacities of Microbial Species and their Interactions. Microorganisms 2020, 8, 840.

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