No one takes a molecule from a bacterium or fungus and then starts giving it to patients. You have to find the specific compound that allows the fungus/bacterium to kill its neighbors--a very labor intensive process. Then you have to get its structure. Then you test it to see if is druggable--will it last long enough in the bloodstream to be effective, for example. It probably isn't, so then you need to synthesize analogs and test them. Then you have to test it for toxicity, maybe synthesize more analogs to get around toxicity problems. And then you can start clinical trials--three rounds of them usually. Somewhere along the way you need to devise a way to make the compound in large enough quantities to turn it into a pill or injection or whatever deliverable form you're picking.
So there are a lot of steps between "hey this compound from this fungus killed that bacteria," and "take this pill once a day for 10 days."