Fecal Microbiota Transplantation Achieves Greater Restoration of Microbiota Diversity and Higher Butyrate Production than Fidaxomicin
This project characterizes the impact of fidaxomicin (FDX) and lyophilized fecal microbiota transplantation (FMT) capsules (EUTEGRA/MBK-01) on the gut microbiota of adult patients with recurrent Clostridioides difficile infection (rCDI), within the framework of the phase III ICD-01 clinical trial (EudraCT 2020-004591-17). Paired stool samples were collected at baseline (active infection) and eight weeks after therapeutic intervention from 27 patients (FDX, n=15; FMT, n=12). Shotgun metagenomic sequencing (Illumina NovaSeq X Plus) was performed on all samples to characterize microbiota taxonomic composition, alpha/beta diversity, functional pathways, C. difficile abundance and toxin-gene burden, and the fecal antibiotic-resistance gene reservoir. A subset of seven patients was additionally profiled by metatranscriptomics to assess the transcriptional activity of key microbial pathways. This dataset provides the raw paired-end shotgun metagenomic and metatranscriptomic reads underlying the comparison of the ecological and functional effects of an antibiotic-based versus a microbiota-based therapy for rCDI.