For a study, it was determined that the elderly in nursing homes (NHs) were disproportionally affected by Clostridioides difficile. The study aimed to look at how other clinical variables are linked to C. difficile colonization and to see how common is C.difficile in NH elders. Residents of New Hampshire provided the researchers with serial stool samples. Quantitative polymerase chain reaction detection of the Toxin genes tcdA and tcdB was used by the researchers to measure the prevalence of C. difficile, and shotgun metagenomic sequencing was used to determine the microbiome makeup. While adjusting for clinical factors such as demographics, medications, and previous medical history, the researchers utilized a mixed-effect random forest modeling engine to identify bacterial taxa whose abundance is related to C. difficile prevalence. About 167 seniors were enlisted, who provided 506 stool samples. Around 30 (24.4%) of the 123 elders who provided multiple samples had multiple C. difficile positive samples, and 78 (46.7%) had at least one C. difficile positive sample. Elderly persons with C. difficile infections had higher counts of pathogenic and inflammatory-associated bacterial species and lower counts of anti-inflammatory and symbiotic bacterial species. Lower prevalence of C. difficile (OR 0.46; 95% CI 0.22–0.99) and PPI (Proton pump inhibitor) usage was linked. And the number of bacteria with known positive effects was significantly lower in elders with high C. difficile prevalence and higher in PPI users. C. difficile colonization was common among the NH elderly, and a dysbiotic gut microbiome was linked to C. difficile colonization. Therefore, a crucial method for reducing C. difficile in the NH is the manipulation of the gut microbiome.