Tal Ofir, Selvaraj Gopinath, Medina Shlomit, Ofaim Shany, Freilich Shiri
Institute of Plant Sciences, Newe Ya'ar Research Center, The Agricultural Research Organization, Ramat Yishay 30095, Israel.
Microorganisms. 2020 Jun 3;8(6):840. doi: 10.3390/microorganisms8060840.
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 Liberibacter solanacearum to those of their culturable taxonomic relative . Second, we demonstrated the potential production of complementary metabolites by pairwise combinations of co-occurring endosymbionts of the plant phloem-feeding whitefly . NetMet, a new web-based tool, is available at https://freilich-lab-tools.com/.
代谢转化使生物体能够利用环境中可获取的营养物质产生一系列必需的代谢产物，这通常需要共生生物之间进行代谢交换。基于基因组的代谢模拟正越来越多地应用于探索代谢能力，同时考虑不同的环境和微生物的不同组合。NetMet是一个基于网络的工具和软件包，用于预测微生物及其在用户定义环境中的相应组合的代谢性能。该算法将（i）物种特异性酶促反应（酶委员会编号）列表和（ii）相关代谢环境列表作为输入。该算法生成的输出包括：（i）单个物种在每个给定环境中可以产生的化合物列表，以及（ii）预计通过互补相互作用产生的化合物列表。该工具在两个案例研究中得到了验证。首先，我们将 obligatory fruit and vegetable pathogen Liberibacter solanacearum不同单倍型与其可培养的分类学相关菌株的代谢能力进行了比较。其次，我们展示了取食植物韧皮部的粉虱共生内共生体成对组合产生互补代谢产物的潜力。NetMet是一个新的基于网络的工具，可在https://freilich-lab-tools.com/获取。
