Community compartment structure - separate-vs-combined extracellular space

[robert-clegg-tessella]

Hello, thank you for this really useful tool 😄

I've done some digging through the paper, the codebase, the documentation, and the discussions but couldn't find an answer to my question. Please point me in the right direction if I've missed it!

I'm trying to simulate a community of a subset of species from the AGORA2 dataset within custom-defined media. I get unexpected results, where growth is lower in the medium that should have more, and vice versa. I think this is because when I use my more comprehensive medium definition (i.e., where many more metabolites have defined fluxes), the flux upper limit on critical metabolites is set to some small value, whereas when I use the more restrictive medium definition these flux upper limits are left at the default (1000).

All of this has made me inspect my sample.compartments more closely. For each species, I have a c_... (cytoplasm), p_... (periplasm), and an e_... (extracellular space) compartment, plus a m (medium) compartment that is shared between all species. This all makes sense to me except for the e_... compartments: shouldn't there be a shared e compartment for all species? Transport reactions including the m compartment are all to individual e_... compartments, meaning that any flux of metabolites between species must currently go through the m compartment, which has flux limits on it due to the medium definition. If there were a shared e compartment with no (or very high) upper bounds on flux, this exchange of metabolites wouldn't be limited by the flux limits associated with the medium definition.

Have I fundamentally misunderstood something, or have I set up my community incorrectly? Many thanks in advance for any help you're able to offer!