You don't eat it, don't be silly.... you stick the poop up your butt
(They run a tube through your nose, down your throat, through the stomach to the top of the intestines, and introduce the bacterial slurry there.)
Also, "fecal transplant" is marketable only to weirdos. "Probiotic infusion" would work better.
For those who want to gain some artistic talent, there's this (but is expensive):
You want to land a substantial amount of, ahem, shit in there, since don't just want it to colonize one portion of the gut, and it's got quite a lot of competition.
So you would be talking a truly astonishing number of pills, I think, to compare to the volume you can manage with a tube.
WP suggests that it's about 100g (or 100000mg) of actual feces then mixed in a larger volume of saline or milk, and you'd probably need to have additional volume for assumed losses and whatever coating you think would work.
That is a _huge_ amount to put in pills.
The shortest safe path is via the nostril.