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Background Fecal microbiota transplantation (FMT) has emerged as a promising therapeutic strategy for the treatment of inflammatory bowel disease (IBD). However, accumulating clinical evidence indicates that the efficacy of FMT is variable and often limited. Donor microbiota composition has been identified as the most critical determinant of treatment response. Thus, optimizing donor microbiota to enhance FMT efficacy represents a clinically relevant and promising avenue for research.Methods In this study, we developed an optimized FMT formulation through in vitro co-fermentation of low molecular weight heparin (LMWH) with gut microbiota derived from FMT donors. Using a dextran sulfate sodium (DSS)-induced colitis mouse model, we assessed the therapeutic effects of this modified FMT and investigated the underlying mechanisms. Integrated metagenomic and metabolomic analyses of in vivo and in vitro samples identified Bacteroides thetaiotaomicron (B.t) as a key bacterial species and 7-ketolithocholic acid (7-KLCA) as its associated metabolite. Genomic analysis and in vitro bacterial cultures further validated the relationship among LMWH, B.t, and 7-KLCA. Additionally, based on mouse transcriptomic profiling, neutrophils were identified as a potential target. The molecular link between 7-KLCA and neutrophil function was elucidated using immunofluorescence, Western blotting, qPCR, and ELISA.Results Our findings demonstrate that LMWH interacts with Bacteroides species, reducing inter-donor microbiota heterogeneity. FMT enhanced by co-fermentation with donor bacteria significantly alleviated DSS-induced colitis in mice and improved the efficacy of conventional FMT. This modified FMT enriched the abundance of B.t, which produces 7-KLCA. Mechanistically, 7-KLCA inhibits glycolysis in activated neutrophils via the FXR signaling pathway, thereby suppressing the formation of neutrophil extracellular traps (NETs).Conclusions LMWH enhances the therapeutic efficacy of conventional FMT by enriching B.t and its metabolite 7-KLCA. This metabolite attenuates NET formation through an FXR-dependent mechanism, offering a novel strategy to optimize FMT for the treatment of IBD.