Background: Many studies have reported significant changes in intestinal microbiota in irritable bowel syndrome (IBS) patients based on quantitative real-time PCR analysis. Aims: We aimed to review the alterations in intestinal microbiota. Methods: An online search up to June 9, 2016, was conducted. This systematic review and meta-analysis included differential expression of intestinal microbiota in patients with IBS versus healthy controls (HCs) and subgroup analysis. We assessed the quality of the included studies using an original assessment tool. Results: A total of 13 articles involving 360 IBS patients and 268 healthy controls were included. The quality assessment scores for these articles ranged from 5 to 8. Significant differences in expression in IBS patients were observed for Lactobacillus (SMD=-0.85, P < 0.001, I-2=28%), Bifidobacterium (SMD=-1.17, P < 0.001, I-2=79.3%), and Faecalibacterium prausnitzii (SMD=-1.05, P < 0.001, I-2=0.0%) but not Bacteroides-Prevotella group, Escherichia coli or other genera or species. Subgroup analysis showed that diarrhea-predominant IBS patients had significantly different expression of Lactobacillus (SMD=-1.81, P < 0.001) and Bifidobacterium (SMD=-1.45, P < 0.001). Conclusion: Down-regulation of bacterial colonization including Lactobacillus, Bifidobacterium and F. prausnitzii was observed in IBS patients, particularly in diarrhea-predominant IBS (IBS-D). Microbiota changes participate in the pathogenesis of IBS and may underlie the efficacy of probiotic supplements. (C) 2017 Editrice Gastroenterologica Italiana S.r.l. Published by Elsevier Ltd. All rights reserved.