Historically, such fecal transplantation (aka fecal bacteriotherapy) was performed via multiple infusions via enema (uncomfortable for both the physician as well as the patient) or via colonoscope. Although first described being done in humans in 1958, it was never really seriously studied until the mid-1980's. Even before humans, it had been performed in animals by veterinarians for centuries.
In any case, there has been new literature supporting the use of nasoduodenal tubes to administer poop via the nose. With nasoduodenal tubes, a tube is threaded through the nose, past the stomach, and into the small bowel.
Now keep in mind that the stool actually NEVER comes into contact with the nose. It is contained within an impermeable tube at all times, so it is not quite as gross as you might think (though mentally, there may still be an emotional ick factor present).
Another approach being considered is encapsulating the poop inside enteric-coated capsules so a patient can theoretically swallow the pill-containing poop.
Media Mention:
Doctors save patient from deadly superbug by transplanting faeces through his NOSE. MailOnline
Reference:
Duodenal infusion of donor feces for recurrent Clostridium difficile. New England Journal of Medicine. 2013 Jan 31;368(5):407-15. doi: 10.1056/NEJMoa1205037. Epub 2013 Jan 16.
Same poop, different gut. The Scientist 11/3/105/2/13
