Question in Microbiome Modeling Toolbox -- Metabolites by Taxa Level Production

[Xinyi Chen]

Hello,

I am working with the mgpipe function from the Microbiome Modeling Toolbox and would like to know the species/strains that produce the metabolites that are secreted out. 

My method is trying to find the metabolites that are secreted out and exist in lumen compartment (with reaction similar to 'h2[u] <=> panParabacteroides_merdae_h2[u] '), having a positive s*flux indicating production. The problem I am facing is I don't know how to extract the flux of reactions in each sample, as I have models for each sample as the output, which contains stochiomatric matrix but no flux values.

I am also asking to see if there are other more convinient methods to get the species/strains?

Thanks a lot!

Best wishes,

Xinyi

[Almut Heinken]

Hello,

if you want to know what the microbe community as a whole is producing, have a look at the output "inputDiet_net_secretion_fluxes.csv".

If you want to know what individual microbes contribute to metabolites, you can use the function "predictMicrobeContributions". You can compute the contributions to all metabolites (takes a long time) or define a set of metabolites of interest.

Best regards,

Almut

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[Xinyi Chen]

Thank you so much!