Clostridioides difficile infection (CDI) remains a major global health challenge, driven by complex interactions among pathogen virulence, host susceptibility, and microbiome disruption. Despite progress, key gaps remain in understanding disease mechanisms and developing durable prevention and treatment strategies. This Topical Collection highlights innovative, reproducible, and translational approaches that are advancing CDI research.

We welcome submissions describing advanced experimental models, including intestinal organoids, microfluidic gut systems, and gnotobiotic or conventional animal models, to study spore germination, toxin activity, and colonization resistance. Protocols integrating real-time imaging and multi-omics approaches, such as metagenomics, metabolomics, and spatial transcriptomics, are particularly encouraged to elucidate host–pathogen–microbiome interactions.

The collection will also feature methodologies for prevention and therapeutics, including evaluation of antibiotics, toxin-neutralizing agents, bacteriophages, and microbiota-based interventions such as defined microbial consortia and fecal microbiota transplantation. Approaches to assess gut barrier function, immune responses, and long-term microbiome recovery are of strong interest.

By providing robust and accessible protocols, this collection aims to enhance rigor and reproducibility, accelerate mechanistic discovery, and support the development of effective, mechanism-based interventions for CDI and recurrent CDI.