The domesticated E.Coli is the biggest hit so far. It is easy to cultivate and is harmless (most of the time). E.Coli has been used to produce therapies like insulin, antibiotics, enzymes, vaccines and so forth. The world as we know it would cease to exist if we took out E.Coli out of the equation.
If we look at our future big hits with microbes, what would they be? Microbes might be used to degrade pesticides. Viruses might also be used instead of pesticides killing off insects. Just as in Turkey, where the king hired Vikings to fight of the attacks of other Vikings, nice fungi might be used to fight of bad fungi.
There are microbes that feed on oil that could be used to clean up big oil spills. Some microbes can produce light. Kits are being developed to use microbes to analyze pollution in water. The health industry is on the track, producing drinks with “nice” microbe strains.
Could they in the future be included in beauty products? “Hey wait a minute, I need to viral spray my hair”. "Where is my microbe cream?" Why not? I am sure there is a bacteria that feed on wrinkles J