A microbial signature for Crohn's disease

Abstract

ObjectiveA 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.DesignWe 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.ResultsIn 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.ConclusionsAlthough 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.

Analysis of endoscopic brush samples identified mucosa-associated dysbiosis in inflammatory bowel disease

“…Comparative analysis using the weighted UniFrac distance indicated that the difference between CD and non-IBD controls was more marked than that between UC and non-IBD controls. These observations are compatible with the results of previous studies of fecal samples [33,34]. A focal alteration of the microbial structure within the inflamed mucosa of IBD has been reported previously [35].…”

Robust Microbiota-Based Diagnostics for Inflammatory Bowel Disease

“…This was recently demonstrated by Pascal et al (14), who identified a unique microbial signature consisting of eight microbial markers for CD that was successfully validated in various different cohorts. However, when applied to a data set processed by a different methodological approach, their method achieved poor accuracy.…”

“…First, we used healthy children as controls, whereas clinicians need to discriminate IBD patients from those with other GI complaints or diseases. As for the cases, we decided, on the basis of our classification and perturbations results, to combine UC and CD patients into one IBD group, even though they were recently described as two distinct subtypes of IBD at the microbiota level (14). In addition, all of the IBD patients in our cohort were in the active state of the disease, so our model cannot be extrapolated to a remission state of IBD.…”

“…The ability to reproduce the within-dataset accuracy with a between-hospital cross-validation is important, since batch effects are quite common in microbiota studies (15,16). These effects have been shown to significantly impact predictive accuracy in microbiota-based predictive models of obesity (25) and CD (14).…”

The contribution of microbial biotechnology to sustainable development goals: microbiome therapies

“…For example, patients with IBD have a gut microbiome characterized by depletion or over‐abundance of specific taxa compared to healthy controls(Pascal et al ., 2017). Based on observations that Clostridia group IV and XIVa species in particular are less abundant in patients with IBD (Manichanh et al ., 2006), one such organism Faecalibacterium prausnitzii is being investigated as a candidate LBP for IBD, following up on promising findings in pre‐clinical colitis models (Sokol et al ., 2008).…”