Rumen transfaunation, the harvesting of rumen fluid from a healthy bovine and administering this to one with rumen dysfunction, has been a tried and true treatment for decades in veterinary medicine. Administering a poop slurry from a healthy horse to one with chronic diarrhea sometimes helped. We were operating on a very macro level (Hey, let’s give it some poop and see if it gets better), and after all these years, with all the sophisticated tools available, I think it’s pretty much the same. I’ve seen lots of studies identifying “good” and “ bad” bacteria, and to your point, I’m left wondering, “So what?”

I think probiotics are mostly commercial hype. However, there is definitely something there when it comes to the potential for a therapeutic benefit to manipulating the microbiome. It will take years of arduous research to get there, though. You may be right to avoid this area for PhD research. Very difficult to define a clear, specific objective to investigate one or two variables. It is biology at its finest in its complexity and elegance, yet most vexing for researchers.