Increased Faecalibacterium abundance is associated with clinical improvement in patients receiving rifaximin treatment

Benef Microbes. 2020 Oct 12;11(6):519-525. doi: 10.3920/BM2019.0171. Epub 2020 Sep 4.


Compositional and functional alterations of the gut microbiota are involved in the pathogenesis of several gastrointestinal diseases. Rifaximin is often used to induce disease remission due to its eubiotic effects on the gut microbiota. To investigate the correlation between changes in the gut microbiota composition and symptoms improvement in patients who present a clinical response to rifaximin treatment. Patients with ulcerative colitis (UC), Crohn's disease (CD), irritable bowel syndrome (IBS) and diverticular disease (DD) undergoing rifaximin treatment for clinical indication were enrolled in the study. Rifaximin was administered at the dose of 1,200 mg/day for 10 days. Faecal samples were collected at baseline and at the end of treatment; clinical improvement was assessed by Mayo score for UC, CD Activity Index (CDAI) for CD, IBS severity scoring system (IBS-SSS) for IBS and global symptomatic score (GSS) for DD. Twenty-five patients were included in the analysis and a clinical improvement was recorded for 10/25 (40%) of them. Microbial alpha diversity showed a slight increase in clinical responders (P=0.271), while it decreased in patients who did not improved (P=0.05). A significant post-treatment increase in Faecalibacterium abundance was observed in patients with a positive response (log2FC 1.959, P=0.042). Roseburia abundance decreased in both groups, whereas Ruminococcus decreased only in patients who clinically improved. Clinical improvement consequent to rifaximin treatment is associated with an increase in Faecalibacterium abundance. Achieving a positive shift in the gut microbiota composition seems a key event to obtain a clinical benefit from treatment.

Keywords: Faecalibacterium; clinical response; eubiotic; gut microbiota; rifaximin.

Publication types

  • Observational Study

MeSH terms

  • Adult
  • Bacterial Load / drug effects
  • Bacteroidetes / growth & development
  • Clostridiales / growth & development
  • Diverticular Diseases / drug therapy*
  • Diverticular Diseases / microbiology
  • Faecalibacterium / growth & development*
  • Female
  • Gastrointestinal Agents / therapeutic use*
  • Gastrointestinal Microbiome / drug effects*
  • Humans
  • Inflammatory Bowel Diseases / drug therapy*
  • Inflammatory Bowel Diseases / microbiology
  • Irritable Bowel Syndrome / drug therapy*
  • Irritable Bowel Syndrome / microbiology
  • Male
  • Middle Aged
  • Rifaximin / therapeutic use*


  • Gastrointestinal Agents
  • Rifaximin