Clarification about _m medium exchanges vs sum ([e]) in the net vs secreted fluxes

[nickp60]

Hello! I am sorry but I am still having a bit of confusion about metabolite net flux vs secretion vs production. This discussion #135 says that the secretion can be obtained by the production_rates function. The production_rates function excludes the medium _m exchanges. However, my confusion comes from the plot_exchanges_from_sample function, which appears to only plot the medium's exchanges? ? I happened across this as butyrate is absent from a plot I generated with plot_exchanges_from_sample(growth, direction="export"), but butyrate is being produced according to the production_rates function. Butyrate isn't being provided by the medium. The export_rates_plot function from the paper seems to show the same behaviour as the production_rates function.

I'm also a little confused by the note in the comments for the production_rates and consumption_rates functions, stating

The net rates can be obtained directly by inspecting the exchange fluxes in the "medium" compartment`

So is the _m designation in the exchanges that which is being provided by the medium, or is that the net from the production/consumption across bugs?

Thanks in advance, sorry for not following!

Nick

[cdiener]

Production is the total flux that is produced and secreted into the shared environment. Consumption is the total flux that is taken in from the environment. The (net) exchanges is denoted by _m the inflow (coming from diet or host) or the outflow fron the environment into the outside. Because of the steady state for each metabolite net exchange = production - consumption. Because the host could in theory also take in metabolites from the shared environment (competing with the bugs) we consider the production fluxes the most relevant for the hostm

[nickp60]

Thanks for your reply! So is this correct?

• production_rates: whats being secreted to the environment from the community
• plot_exchanges_per_sample, direction="import": what medium components decrease in the shared environment due to having more community consumption than community production
• plot_exchanges_per_sample, direction="export": what medium components increase in the shared environment due to having less community consumption than community production.

Does plot_exchanges_per_sample direction=export include all produced metabolites or just the ones that were in the original medium?

Thanks again!

[cdiener]

Hi, so for export everything is like you said. It does include metabolites made by microbes. The plotting if exchanges per sample was originally thought to show variability in the nutrient requirements for each sample. But it seemed odd to not allow plotting the reverse so I added the option. For production and consumption it made more sense to me to have it in reference to some metadata. But if you have an example usage for a projection of production and consumption rates we could definitely add this to plot_exchanges_per_sample.

For import those are metabolites that are coming in from the outside so they are exclusively from the medium, usually the diet and the host, and not made by microbes.