Host-rumen-microbe interactions are essential components of many physiological processes, and therefore can affect ruminant health. Classical knowledge of rumen microbiology is based on culture-dependent methodologies, which only account for 10–20% of the rumen bacterial communities. While, the advancement in DNA sequencing and bioinformatics platforms provide novel approaches to investigate the composition and dynamics of the rumen microbiota. Recent studies demonstrated that the ruminal ecosystem is highly diverse and harbors numerous microbial communities. The composition of these microbial communities are affected by various environmental factors such as nutrition and different management strategies. Disturbance in the microbial ecology of the rumen is associated with the development of various diseases. Despite the flow of recent rumen-based studies, rumen microbiota is still not …