Human health relies on the composition of microbiota in an individual’s gut and the synthesized metabolites that may alter the gut environment. Gut microbiota and faecal metabolites are involved in several gastrointestinal diseases. In this study, 16S rRNA-specific denaturing gradient gel electrophoresis and quantitative PCR analysis showed that the mean similarity of total bacteria was significantly different (P<0.001) in faecal samples from patients with irritable bowel syndrome (IBS; n = 11) and from non-IBS (nIBS) patients (n = 8). IBS subjects had a significantly higher diversity of total bacteria, as measured by the Shannon index (H′) (3.36<H′<4.37, P = 0.004), Bacteroidetes and lactobacilli; however, less diversity was observed for Bifidobacter (1.7< H′<3.08, P<0.05) and Clostridium coccoides (0.9< H′<2.98, P = 0.007). In this study, no significant difference was found in total bacterial quantity (P>0.05). GC/MS-based multivariate analysis delineated the faecal metabolites of IBS from nIBS samples. Elevated levels of amino acids (alanine and pyroglutamic acid) and phenolic compounds (hydroxyphenyl acetate and hydroxyphenyl propionate) were found in IBS. These results were highly correlated with the abundance of lactobacilli and Clostridium, which indicates an altered metabolism rate associated with these gut micro-organisms. A higher diversity of Bacteroidetes and Lactobacillus groups in IBS faecal samples also correlated with the respective total quantity. In addition, these changes altered protein and carbohydrate energy metabolism in the gut.