I am not totally ignorant of this subject, but I'd be concerned about the unknowns involved in messing around with the very long term coevolution of gut biomes with particular diets, groups of people, and factors we might not know about yet. For one example, I don't believe that that gut viromes, the ecosystem of viruses that infect the gut biome bacteria, are very well understood.

There is real wisdom in "do no harm" as a principle. It would be a lot better for most people to lose weight, eat more fruits and vegetables, spend more time outdoors, and sleep more before they consider a prophylactic fecal transplant.