Abstract
Recurrent Clostridium difficile infection (RCDI) remains a significant clinical challenge, with high recurrence rates following standard antibiotic therapy. Emerging evidence supports the role of fecal microbiota transplant (FMT) and standardized microbiome therapeutics (e.g., SER-109, RBX2660) in gut microbiota restoration and recurrence prevention. This systematic review evaluates the effectiveness and safety of these approaches in comparison to traditional therapies. Following the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) 2020 guidelines, we searched the databases PubMed/MEDLINE, ScienceDirect, Cochrane Library, Europe PubMed Central (Europe PMC), ClinicalTrials.gov, Google Scholar, and Elicit AI for studies published between January 2015 and May 2025. Eligible studies included randomized controlled trials (RCTs), observational studies, and case series assessing FMT in adults with rCDI. The risk of bias was assessed using the Cochrane Risk of Bias 2.0 tool (RoB 2) for RCTs and the Newcastle-Ottawa Scale (NOS) for cohort studies. Seven studies (six RCTs, one cohort; N=1,030 patients) were included. FMT demonstrated superior efficacy compared to antibiotics/placebo, with clinical cure rates ranging from 70% to 91% (versus 23% to 62%). Donor FMT outperformed autologous FMT (90.9% vs. 62.5%, p = 0.042) and standard therapies (71% resolution vs. 33% fidaxomicin/19% vancomycin, p < 0.01). Microbiota-based therapies (SER-109, RBX2660) demonstrated comparable efficacy (RRR up to 68%). Safety profiles were favorable, with predominantly mild gastrointestinal events and no increased risk detected for the specific outcomes measured over a five-year follow-up period. Heterogeneity existed in administration routes (colonoscopy/capsules) and donor material (fresh/frozen). FMT and standardized microbiome therapies are highly effective for treating rCDI, demonstrating robust short-term efficacy and favorable long-term safety. Donor-derived interventions and pharmaceutical-grade products (SER-109, RBX2660) represent promising alternatives to traditional antibiotics, particularly in recurrent or refractory cases. Future research should aim to standardize protocols and include more high-risk populations.