I was part of genetics boom when sequencing dropped in price, and I thought that situations just like this were what the market was poised to capitalize on, sequencers in every doctors office or at least cheap enough and prolific enough that sequencing a micriobiome would give doctors data to work with.
The sad reality is that many doctors are operating with what data scientists would reject as missing or bad data, the solution (ignoring the money side) is to get them into a pattern of collecting more data and being better at analysing it.
Each microbiome is different, and I think until sequenced and analyzed, it is simply guessing on the part of patient and doctor.