During the First World War many German soldiers on the Western Front suffered from dysentry. The physician Alfred Nissle compared sick and healthy soldiers and figured that the intestinal bacteria were significantly different. Reasoning that perhaps the bacteria from the healthy soldiers might contribute to healing the sick, he isolated a strain called Escherichia coli Nissle 1917.
U Sonnenborn: "Escherichia coli strain Nissle 1917-from bench to bedside and back: history of a special Escherichia coli strain with probiotic properties.", FEMS Microbiol Lett. 2016 Oct;363(19). pii: fnw212. Epub 2016 Sep 11.
The idea is exactly the same as with modern probiotics, like yoghurt drinks etc, and in fact the original strain is still on the market with its original marketing name: Mutaflor (historical summary (PDF) from the company website). I don't know whether this long history of cultivation might be responsible for its relative weakness now for that purpose (Eg "Thus, E. coli Nissle 1917 does not have the capacity to compete effectively with MDREC in the bowel of elderly patients.")
During the war it proved effective and in case of this special treatment of a certain guy, it seems that "the patient" was satisfied and convinced enough to let Morrell go on to prescribe or just administer him the known full arsenal of polytoxicomania.
Since the beginning of the century quite a few researchers played with the idea of using bacteria for therapeutic effects, not in the least because Metchnikoff published a book bout The prolongation of life; optimistic studies in 1908. But I'd say that the doctors at the time were mostly entrenched in a line of thought from Semmelweis to Koch and Pasteur, namely that bacteria "are evil", and therefore the very idea of using them as therapy as a form of heresy. The exact effects, and whether they are beneficial or what, are still under debate today. (Example from 1992). So, while the product was on the market with good track record, its use wasn't as widespread as modern formulations are now.
It is quite difficult to judge the reasoning and motivation Morrell had at the time. The 'medication' was not entirely unusual, being produced not in a private backyard lab but a proper facility, but even most of his contemporaries considered him a quack. So it is entirely within probable possibilities that 'his reasons' were invalid ("A new miracle cure, I swear!")