gapseq
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jotech
community simulation media
Hello, I am going to simulate a community with 3 bacteria, A,B and C. B takes the products of A and C takes the products of B. When generating the models for gapfilling which medium do I use? Do I use the medium of A for all species or the recommended medium for each species? Thanks
There are different approached to this. However, the general goal is to have a gapfill-medium, that contains all essential nutrients to support the growth of the organism. The gapseq-predicted medium can be a good hint.
In your case, if C depends on nutrients provided by B, the gapfill medium of C should contain the metabolite(s) provided by B. Thus, I would recommend to use the gapfill medium that is predicted for each organism or, to merge the predicted media of all three organisms and use the same merged medium for gapfilling of all three organisms.
Sorry again, but I have another question, when running R with de gapfilled models with each predicted medium it is necesarry to supply a medium (arena_subs <- fread("medium.csv"), which medium is the best? I suppose the medium for A species, is it not? Thanks
Yes that is an option (the merging media), but if I use the predicted media...in that case what would be the best medium?
I'm not sure if I get what you want to do. But if you want to use the predicted media but do not want to merge the media for the community simulation, I would propose to use a standard medium defined by essential metabolites from all predicted media plus individual carbon/energy sources and minus the compounds that some members of the community can produce. Does it somehow answer your question?
Yes you are right, but I wonder if we should not also simulate real life. In real life the input medium must contain the inorganic compunds, amino acids and vitamins requiered for all species plus the carbon source of species A and not the other carbon sources of the other species. Is that right? Thanks for the help.