Identification of gut microbiome and transcriptome changes in ulcerative colitis and pouchitis

Pouchitis is the common postoperative complication of ulcerative colitis (UC) and is also considered as inflammatory bowel disease. The aim was to investigate the microbiological and transcriptional differences between the two illnesses. Eighty-five participants were enrolled (37 UC, 15 healthy UC pouches, 15 pouchitis and 18 healthy volunteers) and stool samples were collected. Microbial populations were analyzed by pyrosequencing of 16S ribosomal DNA. Furthermore, transcriptome data of 119 UC and 28 pouch patients were obtained from two data sets for bioinformatics analysis. The results of gut microbiota community analysis showed that with aggravation of UC, intestinal microorganisms were characterized by a gradual decreased in diversity and numbers of butyrate-producing bacteria and <i>Bacteroides</i>. Besides, in addition to the decrease of probiotics, the proliferation of <i>Escherichia–Shigella</i> and <i>Ruminococcus gnavus</i> was observed in pouchitis which is related to multiple infection pathways. The function enrichment of differential expression genes and hub genes, as well as the immunological condition was shown to be distinct using transcriptome bioinformatics analysis between UC and pouchitis. A stronger immune response occurs in UC and may be associated with high expression of tumor necrosis factor and interleukin, while multiple hub genes such as <i>CDK1</i> in pouchitis are associated with cell cycle regulation. The characteristics of gut microbiota disturbance and transcriptome alteration in UC and pouchitis are different. Our findings suggested that pouchitis may have a unique pathogenesis which was separated from UC.