Ileostomy Microbiome Study Design

Adult ileostomy patients without comorbidities were recruited for this interventions study, using specific in- and exclusion criteria (see Supplemental methods “recruitment criteria”). Importantly, to avoid confounding effects on the study endpoints, study subjects were not allowed to consume pro-, pre- or symbiotics, fresh dairy fermented products (such as yogurt, cottage cheese, buttermilk, or soft-raw cheeses) as well as other food products that are fermented (i.e. sauerkraut) during the study period and three months prior to participation in this trial (a list of forbidden products was provided).
Due to a lack of reliable prior art in the investigation of the impact of food-derived bacteria on the small intestinal microbiota, no effect size could be estimated or a priori power calculation could be performed. Therefore, the study was designed as an explorative study, aiming for the inclusion of 15 to 20 subjects fulfilling the inclusion criteria. We recruited 15 subjects with a standard ileostoma, and a single subject with a continent-ileostoma (i.e. Kock pouch). During data analysis, the SI microbiota of the latter individual was drastically different from the rest of the ileostomists and was therefore considered to be a biological outlier that was excluded from further analyses (see “Results” section).