In my world, the Earth's only sentient species is a microscopic protist ( about 75 - 100 μm and living for 5 years ) that is social lives in groups of 50 - 300, and is highly intelligent. To a species like this, would any microorganism be domesticatable or does the lack of intelligence among microorganisms prevent them from being domesticated?
(of an animal) tame and kept as a pet or on a farm. "domesticated dogs"
(of a plant) cultivated for food; naturalized. "domesticated crops"
So intelligence has nothing to do with domestication. We use Bacteria to make cheeses, and yeast to make fermented beverages. So any thing is 'domesticatable'. All you need is to train something to react how you want to certain stimuli or understand how certain stimuli can get you the reactions you want.
Viruses can perhaps be selectively bred (e.g. like dogs are by humans) to have desirable characteristics such as the ability to convert certain organic compounds into nutrition for themselves and their 'host' species. As far as I know viruses are entirely non-intelligent (even deterministic?) in nature.
For instance your protagonist allows a beneficial virus cell to infect him and thus become able to absorb methane gas and turn it into some form of energy his own body can use.
I suppose this would be like a human deliberately contracting a virus that allows him to digest some previously indigestible but highly abundant foodstuff such as grass.
IIRC, domestication is the result of breeding intelligent compliance into animals, so it would probably only work in multicellular organisms. that being said, their are some kinds of bacteria that i believe are easier to work with, if thats what you mean. the most obvious example i can think of would be e. coli, but im sure that there are other species. sorry if that isnt very helpful.