This is one of the things that’s deeply challenging for biology and biochemistry - it’s extremely resistant to the sort of reductionism that works so well for other fields. It’s rare to find a single compound, a single species, or a single pathway that’s responsible enough for an effect to show up in studies of the sort of power that one can muster without a ton of time and money, and as soon as you try to capture synergistic effects, you hit a combinatorial wall quickly. In microbiology, for instance, colonies of different bacterial species are the norm, not the exception, and metabolic pathways that span multiple species are common to the point that trying to isolate a given species’ contribution can miss the effect entirely.