Maintaining a healthy microbiota in calves leads to less immune disturbances as well as increases feed efficiency for optimal growth and production. Although antibiotics decrease populations of beneficial bacteria, they have been commonly fed to livestock at subtherapeutic levels due to the growth promotion and disease prevention that has been associated with their supplementation. Prebiotics, or non-digestible feed ingredients, have been proposed as feed additives that could accomplish the benefits associated with antibiotics without concerns regarding withdrawal times or the potential for resistance development from pathogenic organisms. Prebiotics help maintain a healthy commensal microbial population in the gastrointestinal tract. There is a very complex relationship between diet, intestinal microbiota, their metabolites, and the host immune system, and the intrinsic immunomodulation induced by different ingredients in the diet that needs to be better understood. Dietary changes affect the commensal microbe populations, but the exact mechanism is not known and has recently it has become a quickly growing area of interest to study. This research represents part of a continuing endeavor to better understand the interactions between the host and the commensal microbiota, as well as ways to affect the bacterial community diversity in a way that improves the health and growth of the animal. It also represents a continuing effort to better understand bioactive feedstuffs and their effects on animals at different ages.