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Significance Clostridioides difficile is the leading cause of healthcare-associated diarrhea worldwide following antibiotic treatment. Consequently, there is medical need for novel antibacterial agents acting againstC. difficile that leave the resident microbiota unharmed. The development of such narrow-spectrum antibiotics requires precise knowledge of the mechanisms that fine-tune gene expression to orchestrate the genomic output at each locus in the genome. We address this issue by defining the global transcriptome architecture ofC. difficile including noncoding regulatory elements, many of which are expressed during gut colonization. Our analysis of these regulators provides evidence for the global function of Hfq in sRNA binding and stabilization in a gram-positive bacterium.

An RNA-centric global view of Clostridioides difficile reveals broad activity of Hfq in a clinically important gram-positive bacterium