Matched Metagenomic and Metatranscriptomic Profiling of CDI
Paired metagenomic (MG) and metatranscriptomic (MT) sequencing was performed on stool samples from 100 adults (50 CDI+, 50 CDI-) to address poorly defined functional roles of fungi and cross-kingdom interactions within the gut microbiomes of patients with Clostridioides difficile infection (CDI). Taxonomic composition, functional gene potential and expression, predicted metabolite profiles, and microbial association networks were evaluated to characterize bacterial and fungal community structure and activity. Differential abundance testing, multivariate modeling, and network analyses were applied to identify CDI-associated taxa, pathways, and trans-kingdom interactions.