A microbial signature for Crohn's disease

TLDR

Microbiome studies have linked IBD to altered gut communities, but existing dysbiosis profiles in adult IBD patients are inconsistent and fail to identify clear microbial signatures for Crohn’s disease or ulcerative colitis. The study aimed to compare the faecal microbiome of Crohn’s disease with ulcerative colitis and non‑IBD subjects, proposing biomarkers that discriminate CD from non‑CD across regions. Using 16S rRNA sequencing on 2,045 faecal samples from Spain, Belgium, the UK and Germany, the authors analyzed 115 million sequences in a longitudinal cohort. Eight microbial groups were identified as a specific Crohn’s disease signature, achieving 80 % sensitivity and 94 % specificity against healthy controls, and demonstrating that CD and UC are distinct IBD subtypes at the microbiome level.

Abstract

<h3>Objective</h3> A decade of microbiome studies has linked IBD to an alteration in the gut microbial community of genetically predisposed subjects. However, existing profiles of gut microbiome dysbiosis in adult IBD patients are inconsistent among published studies, and did not allow the identification of microbial signatures for CD and UC. Here, we aimed to compare the faecal microbiome of CD with patients having UC and with non-IBD subjects in a longitudinal study. <h3>Design</h3> We analysed a cohort of 2045 non-IBD and IBD faecal samples from four countries (Spain, Belgium, the UK and Germany), applied a 16S rRNA sequencing approach and analysed a total dataset of 115 million sequences. <h3>Results</h3> In the Spanish cohort, dysbiosis was found significantly greater in patients with CD than with UC, as shown by a more reduced diversity, a less stable microbial community and eight microbial groups were proposed as a specific microbial signature for CD. Tested against the whole cohort, the signature achieved an overall sensitivity of 80% and a specificity of 94%, 94%, 89% and 91% for the detection of CD versus healthy controls, patients with anorexia, IBS and UC, respectively. <h3>Conclusions</h3> Although UC and CD share many epidemiologic, immunologic, therapeutic and clinical features, our results showed that they are two distinct subtypes of IBD at the microbiome level. For the first time, we are proposing microbiomarkers to discriminate between CD and non-CD independently of geographical regions.