Cattle farming is an ancient practice, with roots in the early Neolithic era that has retained a major status in the food industry, with global beef market revenue amounting to $385.7B (as of 2018). Hence, cattle maintenance is essential for catering to the nutritional requirements of modern civilization. This extensive review aims to provide a holistic overview of the cattle microbiome, analyzing the native microbial composition within the respiratory tract, gastrointestinal tract, reproductive tract, and skin of cattle. The dysbiosis associated with various diseases such as bovine respiratory disease, bovine digital dermatitis, mastitis, Johne’s disease, uterine diseases (metritis and endometritis), and metabolic disorders (ruminal acidosis and ketosis) have been discussed. Moreover, various nonantibiotic microbial therapies including phage therapy, prebiotics, and probiotics have been examined as potential means to reduce disease-associated dysbiosis. In general, this review highlights the importance of the microbiome in the maintenance of health in cattle and its potential in alleviating bovine diseases, with an aim to enhance cattle health and production.