The gastrointestinal tract is home to trillions of microbes that are intimately connected with host health, physiology, and metabolism. Understanding the origin of these gut microbes and how they are altered by different feed additives will enhance our ability to manipulate the structure and function of gut microbiota for optimal animal health and production efficacy. This special issue will explore the source of gut microbiota and how various dietary interventions such as in-feed antibiotics, phytochemicals, and bacterial metabolites alter gut microbiota to improve health and performance of poultry. Journal of Animal Science and Biotechnology is a leading open access journal publishing innovative research across agriculture, dairy and animal science.