For additional insight, we are not actually able to fully model a single bacterial culture, gene expression is random and we are barely getting to know one gene at a time when considering dynamics and not just steady state (we also have some idea how to represent an average bacterium's gene expression at steady state, if they were all doing the same thing, but they aren't)

As far as I know, we are actually closer to (less far from) in vitro models where you culture human cells into organs very close to real ones and apply drugs to those organs. I think they already do that with skin for cosmetics but everything else is far away (key word: I think, not sure).