Analysis of endoscopic brush samples identified mucosa-associated dysbiosis in inflammatory bowel disease

J Gastroenterol. 2018 Jan;53(1):95-106. doi: 10.1007/s00535-017-1384-4. Epub 2017 Aug 29.


Background: The mucosa-associated gut microbiota directly modulates epithelial and mucosal function. In this study, we investigated the mucosa-associated microbial community in patients with inflammatory bowel disease (IBD), using endoscopic brush samples.

Methods: A total of 174 mucus samples from 43 patients with ulcerative colitis (UC), 26 with Crohn's disease (CD) and 14 non-IBD controls were obtained by gentle brushing of mucosal surfaces using endoscopic cytology brushes. The gut microbiome was analyzed using 16S rRNA gene sequencing.

Results: There were no significant differences in microbial structure among different anatomical sites (the ileum, cecum and sigmoid colon) within individuals. There was, however, a significant difference in microbial structure between CD, UC and non-IBD controls. The difference between CD and non-IBD controls was more marked than that between UC patients and non-IBD controls. α-Diversity was significantly lower in UC and CD patients than non-IBD controls. When comparing CD patients with non-IBD controls, the phylum Proteobacteria was significantly increased and the phyla Firmicutes and Bacteroidetes were significantly reduced. These included a significant increase in the genera Escherichia, Ruminococcus (R. gnavus), Cetobacterium, Actinobacillus and Enterococcus, and a significant decrease in the genera Faecalibacterium, Coprococcus, Prevotella and Roseburia. Comparisons between CD and UC patients revealed a greater abundance of the genera Escherichia, Ruminococcus (R. gnavus), Clostridium, Cetobacterium, Peptostreptococcus in CD patients, and the genera Faecalibacterium, Blautia, Bifidobacterium, Roseburia and Citrobacter in UC patients.

Conclusions: Mucosa-associated dysbiosis was identified in IBD patients. CD and UC may be distinguishable from the mucosa-associated microbial community structure.

Keywords: 16S rRNA; IBD; Mucosa-associated microbiome.

MeSH terms

  • Adolescent
  • Adult
  • Aged
  • Case-Control Studies
  • Colitis, Ulcerative / microbiology*
  • Crohn Disease / microbiology*
  • Dysbiosis / microbiology*
  • Endoscopy, Gastrointestinal / methods
  • Female
  • Gastrointestinal Microbiome / genetics*
  • Humans
  • Male
  • Middle Aged
  • RNA, Ribosomal, 16S / genetics
  • Young Adult


  • RNA, Ribosomal, 16S