Yes, phages are the natural "antibiotic"/population control for bacteria. https://humanmicrobiome.info/#bacteriophages-phages
Antibiotics can make phages go extinct. https://humanmicrobiome.info/antibiotics/#virome
Phages were being researched as an alternative to antibiotics, but antibiotics seemed easier and cheaper, so they grew in popularity and use. Unfortunately, antibiotics come with pretty severe collateral damage.
Keto is an elimination diet. If you need it, it means you lack the gut microbes required to properly digest other foods.