cdanielmachado
commented
5 years ago When you create a common community biomass reaction, the default objective function for the community is this reaction.
When you don't create a common biomass reaction, the default objective function for the community is the sum of the individual biomass reactions.
But you can easily change this by modifying the coefficients of the objective function. Since there is really no standard way to simulate microbial communities, in the end, it is up to you to choose the most appropriate method.
For instance, you can try multi-objective FBA: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0171744
rdmtinez
Greetings Daniel,
When I run FBA (cobrapy) on a 2-membered community GEM, I notice that the objective value for the community is nothing more than the sum of the individual FBA values of the two GEMs used to create the SyntComm model. I was under the impression that the --no-community-biomass option would produce simulations that allow each member to grow at a different rates, ultimately allowing the simulation of competition. Was I incorrect in my assumption, or am I missing something critical?
It might be noteworthy to point out the following: Individual Strain GEMs were made as follows:
carve --dna bug1.fna --fbc2 -o gem1.xmlmerged comms as follows:
merge_community gem1.xml gem2.xml --no-community-biomass --split-pool --fbc2 -o gem1_gem2.xmlgem1_fba_value = x gem2_fba_value = y gem1_gem2_fba_value = x+y