| Summary: | The objective was to determine the bacterial composition in inflamed and non-inflamed pouches for comparison to the microbiota of healthy individuals. Pouch patients and healthy individuals were included between November 2017 and June 2019 at the Department of Gastrointestinal Surgery, Aalborg University Hospital, Denmark. A faecal sample was collected from all participants for microbiota analysis using 16S rRNA amplicon sequencing. Overall, 38 participants were included in the study. Eleven patients with a normally functioning pouch, 9 patients with chronic pouchitis, 6 patients with familial adenomatous polyposis, and 12 healthy individuals. Patients with chronic pouchitis had overall lower microbial diversity and richness compared to patients with a normal pouch function (<i>p</i> < 0.001 and <i>p</i> = 0.009) and healthy individuals (<i>p</i> < 0.001 and <i>p</i> < 0.001). No significant difference was found between patients with familial adenomatous polyposis and chronic pouchitis (microbial diversity <i>p</i> = 0.39 and richness <i>p</i> = 0.78). Several taxa from the family <i>Enterobacteriaceae</i>, especially genus <i>Escherichia</i>, were associated primarily with patients with chronic pouchitis, while taxa from the genus <i>Bacteroides</i> primarily were associated with healthy individuals and patients with a normally functioning pouch. Finally, a microbial composition gradient could be established from healthy individuals through patients with normal pouch function and familial adenomatous polyposis to patients with chronic pouchitis.
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