Evaluation of Clinical Practice Guidelines on Fecal Microbiota Transplantation in Adults: A Cross-Sectional Study

Fecal microbiota transplantation (FMT) is an emerging multi-disease therapy, yet the quality and consistency of its available clinical practice guidelines (CPGs) remain unknown. This study aimed to systematically evaluate the quality, content coverage and recommendation consistency of FMT-related guidelines and develop an optimization framework for evidence-informed future guideline revision and standardized FMT clinical practice.

We searched PubMed, Embase, Web of Science Core Collection, The Cochrane Library, CNKI, WanFang Data, and official websites of guideline development organizations and professional societies from inception to March 11, 2026. Two reviewers independently screened and selected CPGs with actionable recommendations and conducted quality evaluation via the Appraisal of Guidelines for Research & Evaluation (AGREE) II instrument. Intraclass correlation coefficient (ICC) with 95% confidence intervals (CIs) was computed for each AGREE II domain and interpreted according to Fleiss' criteria. Inter-guideline agreement was reported as the percentage of CPGs endorsing each recommendation.

Eighteen CPGs (3 general, 15 FMT-specific) with 191 recommendations were included. Applicability obtained the lowest AGREE II score (37.8%), followed by rigor of development (47.4%) and stakeholder involvement (49.7%). General guidelines scored higher than FMT-specific guidelines in applicability (62.5% vs. 32.9%) and stakeholder involvement (59.3% vs. 47.8%), but lower in rigor of development (38.9% vs. 49.1%). The coverage of recommendations showed marked inter‑guideline heterogeneity. Recurrent Clostridioides difficile infection (rCDI) was the most consistently recommended indication with the highest level of evidence (10/16). Over 75% of guidelines ignored transplant-center management, and non-CDI indications and key operational steps lacked sufficient high-certainty evidence. ICCs (0.86-0.97) showed excellent evaluator consistency.

Current FMT guidelines exhibit significant methodological deficiencies, heterogeneous recommendation coverage, and limited consensus beyond rCDI. FMT-specific guidelines show better developmental rigor but poorer applicability than general guidelines. Future FMT guideline development should establish core topic sets, adopt multidisciplinary collaborative mechanisms, and develop implementation toolkits with regular update protocols.