Well, there is always the problem of keeping just the right bacteria. In the video the idea seems to be that they are looking for broad spectrum replacements for our current antibiotics. But using broad spectrum antibiotics may be causing some of our current health problems. So we have to be really careful how we use antibiotics. They are extremely valuable to cure a host of really bad diseases, but as shown in the SciAm article, they can also lead to some side effects that may lead to a lot of other problems.
It looks to me as though we really need to be trying to find some very specific treatments. So if you have TB, for example, they give you the TB treatment, and it doesn't impact the other bacteria. It seems as though the ideas discussed in the video might be adaptable to that sort of thing.
Of course then we run into the problem that pharmacies would have to stock thousands of special purpose medicines that may only be used a few times a year. That can lead to some serious problems with having what you need when you need it.
Bill Gill