Comment by caublestone

Bacteriophages lost out to antibiotics in the 1950s. Designing bacteriophages for specific microbes is fairly straight forward so you could design a probiotic loaded with good bacteria to be delivered with a bacteriophage against bad bacteria to quickly adjust the microbiome ecology towards a desired state. The nice thing is that bacteriophages are dietary supplements so you don't need drug approval (unless cure claims are made).