Questions about the Microbiome Modeling Toolbox mgPipe

[Aarush Garg]

I’ve been working with a microbiome metabolic modeling pipeline that involves constraining community models with dietary inputs, and I had a few conceptual questions I’d appreciate your insights on:

1. Rationale for Maximizing and Minimizing Diet Exchange Fluxes:
   Could you elaborate on the biological or modeling rationale behind maximizing or minimizing the fluxes of diet exchange reactions? I’m particularly interested in understanding how these objectives relate to realistic nutrient availability and uptake behavior.

2. Net Uptake into the Fecal Compartment:
   I came across the term net uptake into the fecal compartment, which struck me as counterintuitive—since feces is an excretion endpoint, not a site of uptake. Could someone clarify what this terminology means in the context of the model? Is this a modeling artifact or a defined convention?

3. Unmapped Compounds:
   What exactly are “unmapped compounds” as referenced in some of the diet processing scripts? Are these compounds metabolites that don’t map to known exchange reactions? Are they required in all diet definitions, and if so, what’s the reasoning behind their inclusion?

4. Micronutrients vs. Essential Metabolites:
   Are micronutrients, as defined in the diet modeling context, synonymous with the essential metabolites specified in functions like adaptDiet, or are they a distinct category with different modeling implications?
   
   

These questions are a result of me trying to understand how the inputDiet_net_secretion and inputDiet_netUptake.csv files are created after the personalized models are stored

[Aarush Garg]

Hello, just following up on this. My PI and I would like to know the rationale behind reporting net_secretion and net_uptake, and if it relates to realistic nutrient availability as opposed to just reporting max_secretion and max_uptake.

Let me know if any more information is needed, or if these questions are unclear, thank you

[Almut Heinken]

Dear Aarush,

thank you for your question. Net uptake and net secretion in this case refers to the net consumption and production of metabolites by the microbiome. Hence, net uptake does not include dietary compounds that are predicted to pass through without being taken up by the microbiome, and net secretion does not include the fraction of metabolite flux into the fecal secretion compartment coming only from the diet. I hope that makes the assumptions by the pipeline clearer. Unmapped compounds and micronutrients refer to the definition of dietary metabolites and mapping to food items in the Diet Designer tool on the Virtual Metabolic Human website. These are not the same as the essential metabolites needed for growth of AGORA2.

I hope this helps,

best regards,

Almut

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