Good article. As someone who did this as part of a supervised trial, the only thing that needs mentioning (and I realize the new yorker is not a science journal) is that most FMT experts actually strongly advise AGAINST using a family member or close friend as a donor. The thought being that since CD is multifactorial in origin and possibly can have an envirormental/diet trigger or at least influence, it is important to use stool from someone completely outside of our little inner worlds. FMTers typically insist on relatives/friends b/c of assurance of lack of disease. However, in controlled trials, the donors are screened for anything and everything beforehand. So that is less of a concern.
I think with FMT it's not just the good vs. bad bacteria. It's about introducing a whole new fecal system that when it interacts with the colon lining, is able to change the trajectory of the inflammatory or immune response. At least that's the thought from those at Harvard, and it's an interesting claim. From close relatives and friends we may get some good bacteria, but other elements of the fecal matter may not be that different, and therefore maybe not as effective.
Also performing by colonsocpy is much preffered at this point over other modalities. The spray is consistent from TI to splenic flexure, more easily held than a "bolus" confined to a small area, and a clear picture of what is going on inside at the moment of FMT is obtained.
But, still good article overall.