Luminal microbiota related to Crohn's disease recurrence after surgery

Background Microbial factors are likely to be involved in the recurrence of Crohn's disease (CD) after bowel resection. We investigated the luminal microbiota before and longitudinally after surgery, in relation to disease recurrence, using 16S metagenomic techniques. Methods In the prospective Post-Operative Crohn's Endoscopic Recurrence (POCER) study, fecal samples were obtained before surgery and 6, 12, and 18 months after surgery from 130 CD patients. Endoscopy was undertaken to detect disease recurrence, defined as Rutgeerts score >= i2, at 6 months in two-thirds of patients and all patients at 18 months after surgery. The V2 region of the 16S rRNA gene was sequenced using Illumina MiSeq. Cluster analysis was performed at family level, assessing microbiome community differences between patients with and without recurrence. Results Six microbial cluster groups were identified. The cluster associated with maintenance of remission was enriched for theLachnospiraceaefamily [adjusted OR 0.47 (0.27-0.82),P= .007]. The OTU diversity ofLachnospiraceaewithin this cluster was significantly greater than in all other clusters. The cluster enriched forEnterobacteriaceaewas associated with an increased risk of disease recurrence [adjusted OR 6.35 (1.24-32.44),P= .026]. OTU diversity ofEnterobacteriaceaewithin this cluster was significantly greater than in other clusters. Conclusions Luminal bacterial communities are associated with protection from, and the occurrence of, Crohn's disease recurrence after surgery. Recurrence may relate to a higher abundance of facultatively anaerobic pathobionts from theEnterobacteriaceaefamily. The ecologic change of depletedLachnospiraceae, a genus of butyrate-producing bacteria, may permit expansion ofEnterobacteriaceaethrough luminal environmental perturbation.