Abstract
Diarrheal disease, a major cause of morbidity and mortality in dairy calves, is strongly associated with the health and composition of the gut microbiota. Clostridioides difficile is an opportunistic pathogen that proliferates and can produce enterotoxins when the host experiences gut dysbiosis. However, even asymptomatic colonization with C. difficile can be associated with differing degrees of microbiota disruption in a range of species, including people, swine, and dogs. Little is known about the interaction between C. difficile and the gut microbiota in dairy calves. In this study, we sought to define microbial features associated with C. difficile colonization in pre-weaned dairy calves less than 2 weeks of age. We characterized the fecal microbiota of 80 calves from 23 different farms using 16S rRNA sequencing and compared the microbiota of C. difficile-positive (n = 24) and C. difficile-negative calves (n = 56). Farm appeared to be the greatest source of variability in the gut microbiota. When controlling for calf age, diet, and farm location, there was no significant difference in Shannon alpha diversity (P = 0.50) or in weighted UniFrac beta diversity (P = 0.19) between C. difficile-positive and-negative calves. However, there was a significant difference in beta diversity as assessed using Bray-Curtiss diversity (P = 0.0077), and C. difficile-positive calves had significantly increased levels of Ruminococcus (gnavus group) (Adj. P = 0.052), Lachnoclostridium (Adj. P = 0.060), Butyricicoccus (Adj. P = 0.060), and Clostridium sensu stricto 2 compared to C. difficile-negative calves. Additionally, C. difficile-positive calves had fewer microbial co-occurrences than C. difficile-negative calves, indicating reduced bacterial synergies. Thus, while C. difficile colonization alone is not associated with dysbiosis and is therefore unlikely to result in an increased likelihood of diarrhea in dairy calves, it may be associated with a more disrupted microbiota.
Highlights
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]
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]
Summary
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]. Given the crucial role of the gut microbiota 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 microbiota is needed. The goal of this cross-sectional study was 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
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