Reduced Abundance of Butyrate-Producing Bacteria Species in the Fecal Microbial Community in Crohn's Disease

Digestion. 2016;93(1):59-65. doi: 10.1159/000441768. Epub 2016 Jan 14.


Background: The global alteration of the gut microbial community (dysbiosis) plays an important role in the pathogenesis of inflammatory bowel diseases (IBDs). However, bacterial species that characterize dysbiosis in IBD remain unclear. In this study, we assessed the alteration of the fecal microbiota profile in patients with Crohn's disease (CD) using 16S rRNA sequencing.

Summary: Fecal samples from 10 inactive CD patients and 10 healthy individuals were subjected to 16S rRNA sequencing. The V3-V4 hypervariable regions of 16S rRNA were sequenced by the Illumina MiSeq™II system. The average of 62,201 reads per CD sample was significantly lower than the average of 73,716 reads per control sample. The genera Bacteroides, Eubacterium, Faecalibacterium and Ruminococcus significantly decreased in CD patients as compared to healthy controls. In contrast, the genera Actinomyces and Bifidobacterium significantly increased in CD patients. At the species level, butyrate-producing bacterial species, such as Blautia faecis, Roseburia inulinivorans, Ruminococcus torques, Clostridium lavalense, Bacteroides uniformis and Faecalibacterium prausnitzii were significantly reduced in CD patients as compared to healthy individuals (p < 0.05). These results of 16S rRNA sequencing were confirmed in additional CD patients (n = 68) and in healthy controls (n = 46) using quantitative PCR. The abundance of Roseburia inulinivorans and Ruminococcus torques was significantly lower in C-reactive protein (CRP)-positive CD patients as compared to CRP-negative CD patients (p < 0.05).

Key message: The dysbiosis of CD patients is characterized by reduced abundance of multiple butyrate-producing bacteria species.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Actinomyces / genetics
  • Actinomyces / metabolism
  • Adult
  • Bacteroides / genetics
  • Bacteroides / metabolism
  • Bifidobacterium / genetics
  • Bifidobacterium / metabolism
  • Butyrates / metabolism
  • Case-Control Studies
  • Clostridium / genetics
  • Clostridium / metabolism
  • Crohn Disease / metabolism
  • Crohn Disease / microbiology*
  • DNA, Bacterial / genetics
  • DNA, Ribosomal / genetics
  • Dysbiosis / metabolism
  • Dysbiosis / microbiology*
  • Eubacterium / genetics
  • Eubacterium / metabolism
  • Feces / microbiology
  • Female
  • Gastrointestinal Microbiome / genetics*
  • Gastrointestinal Microbiome / physiology
  • Humans
  • Male
  • RNA, Ribosomal, 16S / genetics
  • Real-Time Polymerase Chain Reaction
  • Ruminococcus / genetics
  • Ruminococcus / metabolism
  • Sequence Analysis, DNA
  • Sequence Analysis, RNA


  • Butyrates
  • DNA, Bacterial
  • DNA, Ribosomal
  • RNA, Ribosomal, 16S