Prevalence of Clostridium difficile and Clostridium perfringens in Swiss horses with and without gastrointestinal disease and microbiota composition in relation to Clostridium difficile shedding

•Single day samples detected 10% less shedding than cumulative sampling over 3 days.•Horses with colic shed significantly more C. difficile but not C. perfringens.•Prevalence in horses with diarrhea was 8% for both Clostridium species.•Alpha diversity did not differ between C. difficile shedders and non-shedders.•Limited differences were seen on LEfSE analysis and in beta diversity indices. Overgrowth of enteric clostridia in dysbiosis in horses with colic is presumed but scarcely investigated. The objective was to provide prevalence data of Clostridium difficile and Clostridium perfringens in horses with and without gastrointestinal disease in Switzerland, and investigate microbiota differences between C. difficile shedders and non-shedders. Fecal samples were taken from healthy horses (n = 103), horses with colic (n = 98) and horses with diarrhea (n = 151). Colic horses were sampled on three days. Selective enrichment culture and molecular typing for C. difficile and C. perfringens was performed. Microbiota differences between horses with colic shedding (n = 7) and not shedding (n = 7) C. difficile were assessed using metagenomic sequencing. The cumulative prevalence (19% C. difficile; 16% C. perfringens) was higher compared to single day samples (1–10% C. difficile; 3–8% C. perfringens, all p