In the past decades, the research on the gastrointestinal microbiology has been the most active research area, because the gastrointestinal microbes are related not only to the nutritional importance but also to the environmental and public health impacts. This collection of papers review the literature related to the latest advances in antimicrobial usage and resistance in beef production, rumen microbiome associated with methane emissions and its mitigation, gut mucosal immune system, rumen microbial function in degradation of toxic feed composition, microbiota-host interaction at the gut epithelial level, health and nutrition, and prospective strategies to modulate rumen microbes and fermentation. Journal of Animal Science and Biotechnology is a leading open access journal publishing innovative research across agriculture, dairy and animal science.