A few twists and turns to this.
Probiotic bacteria are almost exclusively aerobic, needing oxygen to live, which means they work almost entirely in the upper GI tract.
Fecal bacteria are almost exclusively anaerobic, meaning that oxygen will kill them. But this also means that they are difficult to get into the lower GI and colon.
However, early experiments with fecal transplant were done with what was called “chocolate shake”, which literally was a chocolate shake with a fresh fecal sample added to it, that would get “far enough south” to be out of the high oxygen parts of the GI tract.
Also importantly, the anaerobic bacteria, while good, or even very good, in the lower GI tract and colon, can be very toxic in about any other part of the body.
Add to this that a large part of the staff of the FDA, and the USDA, for that matter, are exceedingly bacteriophobic, meaning that they are scared of any bacteria, and find it hard to imagine that any bacteria could be “good”, much preferring sterility in all things.
As far as the intestinal flora itself, while it typically has between 300-1000 different kinds of bacteria in it, usually only 30-40 take up almost all of the available space.
Science is only beginning to get a grasp on how these bacteria, and the other microorganisms: viruses, fungi, amoebas, parasites, etc. interact with each other and our immune systems. But the bottom line is that they are just as much a part of us as our own cells.
I suspect the FDA will try to inhibit this as much as possible. Once the actual helpful intestinal flora are identified, they won’t bring in much $$$ to big pharma.