This research contained four studies aiming to expand the current knowledge of the etiology, pathogenesis, treatment and prevention of calf diarrhea. The first study of this thesis investigated the detection rates of BCoV in feces of healthy and diarrheic dairy calves. BCoV was more likely to be detected in diarrheic than farm-, season-, aged-matched healthy calves. The second study of this thesis characterized the fecal microbiota of healthy calves and calves with diarrhea from 2 different farms. The fecal microbiota of healthy dairy calves appeared to be farm-specific as were the changes during diarrhea. Significant differences in microbiota structure and membership between healthy and diarrheic calves suggest that dysbiosis occurred in diarrheic calves. The third study evaluated the impact of an algorithm for selection of antimicrobial therapy for diarrheic calves on antimicrobial treatment rates and changes in the fecal microbiota. The implementation of an algorithm resulted in a reduction in antimicrobial treatment rates of 80%, with no identifiable negative impacts on clinical outcomes. The marked reduction in antimicrobial treatment rates coincided with a significant increase of the Bacteroides and multiple butyrate -producing bacteria along with the reduction of members of the phylum Proteobacteria. The last study evaluated the impact of an antimicrobial-use algorithm for treatment of diarrhea antimicrobial usage and calf health in 10 dairy farms from Ontario. The implementation of an algorithm drastically reduced in the number of diarrheic calves treated with antimicrobials (before implementation: 85%, after implementation: 18%; P < 0.001), the total mass of antimicrobials used in the farms, and the use of highly important antimicrobials for human health (e.g. cephalosporins) without impacting negatively the health and welfare of the calves. Our study provided additional support for the role of BCV and dysbiosis in calf diarrhea. Our study also demonstrated that the use of written protocols for treatment of diarrheic calves resulted in a drastic reduction in antimicrobial usage with no negative effects in calf health. Furthermore, the reduction in the use of antimicrobial agents could have a beneficial effect on the gut microbiota.