Objective for individual community strains

[jmol0917]

Is there any way to modify the objective of individual members within a community? e.g. change it from biomass generation to specific metabolite generation?

I understand that community-level objectives can be selected by using com.objective = 'reaction_ID' but is there any option to do this for individual strains that are part of a community.

For example, if I have a community composed of Bacteroides caccae ATCC 43185 and Achromobacter xylosoxidans A8. Is there any way in which I can change the objective of one of these while the other's objective is still to generate biomass? Would modifying the objective of one of these strains using the cobrapy method model.objective work? or is there a way in which the objective can be specified in the dataframe that is passed when building the community: com = Community(taxonomy)?

Thanks

[cdiener]

It's possible, however, I would not recommend using cooperative tradeoff in that case. ctFBA is only valid for growth rates. If you want to optimize growth and the production of a particular metabolite at the same time the recommended strategy would be to first run ctFBA and then maximize the target reaction while maintaining the obtained growth rates.

For instance:

from micom.data import test_taxonomy
from micom.util import _apply_min_growth
from micom import Community

tax = test_taxonomy()
com = Community(tax)
sol = com.cooperative_tradeoff()
with com:
    _apply_min_growth(com, sol.members.growth_rate.drop("medium"))
    com.objective = com.reactions.EX_ac_e__Escherichia_coli_1
    ac_sol = com.optimize()
print(ac_sol.objective_value)

If you just want to optimize the changed objective without any constraint on the growth rates you can do so the same way as in cobrapy and o things like: com.objective = com.reactions.EX_ac_e__Escherichia_coli_1 + com.reactions.EX_ac_e__Escherichia_coli_3 or whatever you like. Note the added taxon name in the reaction ID.

Best

[jmol0917]

Amazing! Thanks for your help!

[sankarmaheshr]

Hi @cdiener .
I was using the above approach to simulate my communities. I observed that whenever I try to enforce an objective function that has 2 reactions (1 from each member of the community) then it throws an error 'NoneType' object has no attribute.
But when I simulate the community with just 1 reaction from one member of the community then it works without throwing any error.
What could possible be the reason for this?