Gut Microbial Diversity Is Reduced in Smokers with Crohn's Disease

Inflamm Bowel Dis. 2016 Sep;22(9):2070-7. doi: 10.1097/MIB.0000000000000875.


Background: Smoking has a negative impact on Crohn's disease (CD), but the mechanisms underlying this association are unclear. We compared the gut microbiota composition of smoking with nonsmoking patients with CD using a metagenomic approach.

Methods: Stool samples and clinical data were collected from current smokers and nonsmokers with CD from France and the Netherlands, matched for country, gender, age, disease activity, and body mass index. Fecal DNA was sequenced on an Illumina HiSeq 2500. On average, 40 million paired-end reads were generated per sample. Gene richness and the Shannon index were computed to assess microbial diversity. Wilcoxon's signed-rank tests for paired samples were performed to detect differences between the 2 groups.

Results: In total, 21 smoking and 21 nonsmoking patients with CD were included. Compared with nonsmoking patients, gut microbial gene richness (P = 0.01), genus diversity (P < 0.01), and species diversity (P = 0.01) were decreased in smoking patients. This was accompanied by a reduced relative abundance of the genera Collinsella (P = 0.02), Enterorhabdus (P = 0.02), and Gordonibacter (P = 0.02) in smokers. No statistically significant differences at the species level were observed, although smokers had lower proportions of Faecalibacterium prausnitzii (P = 0.10).

Conclusions: Gut microbial diversity is reduced in smokers with CD compared with nonsmokers with CD. The microbial profile differs between these groups at the genus level. Future studies should evaluate whether intestinal microbes mediate the adverse effects of smoking in CD.

Publication types

  • Observational Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Bacteria / classification*
  • Bacteria / isolation & purification
  • Case-Control Studies
  • Crohn Disease / microbiology*
  • DNA, Bacterial / genetics
  • Feces / chemistry
  • Feces / microbiology
  • Female
  • France
  • Gastrointestinal Microbiome*
  • Humans
  • Leukocyte L1 Antigen Complex / analysis
  • Male
  • Netherlands
  • Prospective Studies
  • RNA, Ribosomal, 16S / genetics
  • Smoking / adverse effects*


  • DNA, Bacterial
  • Leukocyte L1 Antigen Complex
  • RNA, Ribosomal, 16S