Gut microbiota associations with diet in irritable bowel syndrome and the effect of low FODMAP diet and probiotics

Background and Aims Diet is both a modulator of the gastrointestinal microbiota and an important therapy in irritable bowel syndrome (IBS). We aimed to comprehensively (i) identify diet-microbiota associations in adults with IBS consuming habitual diet; (ii) assess the impact of two nutritional interventions on the microbiota; and (iii) determine whether baseline microbiota can predict clinical response to diet or probiotic intervention. Methods Data were analyzed from 95 individuals with IBS participating in a previously published 4-week 2x2 factorial design randomized controlled trial investigating the impact of the low FODMAP diet (LFD) and co-administration of a probiotic. Diet was assessed at four hierarchical levels and partial 16S rRNA gene sequencing was used to profile the microbiota. Results There were numerous diet-microbiota associations especially at the nutrient level, including a negative association between protein and Bifidobacterium abundance (rs= -0.358, p<0.001). After correction for multiple testing, the significance for this association (q=0.237) and all others was lost. Low FODMAP diet led to changes in abundance of major saccharolytic genera compared with sham diet, including higher Bacteroides (LFD 34.1% (15.7%) vs sham 23.3% (15.2%), q=0.01) and lower Bifidobacterium (0.9% (1.0%) vs 2.1%, (2.5%) q=0.029). Compared with placebo, probiotic supplementation led to higher Lactobacillus (Probiotic 0.08% (0.1%) vs placebo 0.03% (0.2%), q<0.001), and Streptococcus abundance (2.0% (2.2%) vs 0.6% (1.2%), q=0.001). The probiotic treatment buffered the impact of the low FODMAP diet on Bifidobacterium. Baseline microbiota did not predict clinical response to either intervention. Conclusions Although diet modifies the gut microbiota, bivariate correlation analysis may only provide a limited explanation of the complex diet interactions with individual gut bacteria in IBS. Some diet interventions modify the microbiota in IBS. Registered under ISRCTN registry identifier no. ISRCTN02275221.