KEGG pathway analysis for in vitro fermentation systems

MetaboAnalyst
1

Which KEGG reference organism should be used for pathway analysis of metabolites identified from in vitro fermentation of a plant substrate?

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Based on your in vitro fermentation systems and analysis objectives, two possible directions:

  1. Hypothsis testing mode - if you do expect some pathways / enzymes present, choose an organism that contains the reactions => Pathway Analysis module, choose the organims

  2. Discovery mode - if you have no idea, you can just map the metabolites to the KEGG global network => Network Analysis module, choose the “KEGG Global Metabolic Network” see below

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Thank you so much for the reply