Evidence consistency analysis of the effect of a low-FODMAP diet on the abundance of Bifidobacterium and Faecalibacterium prausnitzii in patients with irritable bowel syndrome

Background The low-FODMAP diet is recommended by clinical guidelines as an effective dietary strategy for alleviating symptoms in patients with irritable bowel syndrome (IBS). However, its effect on Bifidobacterium and Faecalibacterium prausnitzii ( F. prausnitzii ) remains unclear, largely due to methodological heterogeneity. Methods We systematically searched the literature up to September 2026 for randomized controlled trials comparing low-FODMAP diets with control diets in adults with IBS. Given the high methodological heterogeneity across studies, we performed a direction-of-effect and consistency analysis (vote counting and sign test) instead of a traditional meta-analysis. Results 12 RCTs were included. For Bifidobacterium (11 studies), 9 (81.8%) reported a decrease and 2 reported no change; the sign test confirmed a consistent reduction ( p = 0.033). A sensitivity analysis including only studies with direct between-group comparisons (9 studies) was consistent with the aforementioned analysis (8 reported a decrease, p = 0.020). For F. prausnitzii (7 studies), the evidence was inconsistent: 2 reported a decrease, 4 reported no change, and 1 reported an increase, with no statistically significant trend. Conclusion Most current evidence indicates that a low FODMAP diet reduces the abundance of Bifidobacterium in IBS patients, while its effect on F. prausnitzii remains unclear. This finding enables clinicians to conduct more evidence-based counseling with patients, clarifying the specific effects (and non-effects) of the low-FODMAP diet on microbiota and facilitating informed decision-making regarding dietary management. Furthermore, future research should investigate the dynamics of microbiota during the reintroduction phase and consider patient microbiota subtypes to clarify the overall impact of the diet on the microbiota. Systematic review registration This systematic review has been registered with PROSPERO (International Prospective Register of Systematic Reviews) under the registration number CRD420261351146. The publicly accessible URL is: https://www.crd.york.ac.uk/PROSPERO/ .