The effects of colonization with Clostridioides difficile on the fecal microbiome of dairy calves

Infectious diarrheal disease is one of the main causes of mortality in dairy calves (1, 2), and calves less than 30 days of age are at highest risk of developing diarrhea (3, 4). Studies have shown that gut microbial composition is associated with gut health and the likelihood of diarrhea: reductions in microbial diversity are associated with an increased incidence of diarrhea (5), and the colonization of the calf gut with beneficial bacteria along with the decreased colonization of potential pathogens decreases the likelihood of calf diarrhea (6). Clostridioides difficile is a spore-forming anaerobic, gram-positive bacillus that is a significant enteric pathogen in many species of animals. Colonization with C. difficile has been shown to be associated with reduced gut microbial diversity and increased colonization of pathogenic bacteria in people (7, 8), and we recently demonstrated a similar association in puppies (9). Dairy calves, like the neonates of other species, are colonized with C. difficile at high rates, with reported prevalences ranging from 28-56% (10, 11). While there is some evidence that infection with C. difficile can result in diarrhea in calves (12), the effect of the asymptomatic colonization of calves on the gut microbiome is unknown. Given the crucial role of the gut microbiome in providing colonization resistance against pathogens that cause diarrhea (13, 14), a better understanding of the effect of pathogens such as C. difficile on the calf gut microbiome is needed. The goal of this study is to define the gut microbiota features associated with C. difficile colonization in dairy calves and to define the effects of calf age, diet, and farm on the risk of colonization.