The fields of immunology, microbiology, and nutrition converge in an astonishing way. Dietary ingredients have a profound effect on the composition of the gut microflora, which in turn regulates the physiology of metazoans. As such, nutritional components of the diet are of critical importance not only for meeting the nutrient requirements of the host, but also for the microbiome. During their coevolution, bacterial microbiota has established multiple mechanisms to influence the eukaryotic host, generally in a beneficial fashion. The microbiome encrypts a variety of metabolic functions that complements the physiology of their hosts. Over a century ago Eli Metchnikoff proposed the revolutionary idea to consume viable bacteria to promote health by modulating the intestinal microflora. The idea is more applicable now than ever, since bacterial antimicrobial resistance has become a serious worldwide problem both in medical and agricultural fields. The impending ban of antibiotics in animal feed due to the current concern over the spread of antibiotic resistance genes makes a compelling case for the development of alternative prophylactics. Nutritional approaches to counteract the debilitating effects of stress and infection may provide producers with useful alternatives to antibiotics. Improving the disease resistance of animals grown without antibiotics will benefit the animals' health, welfare, and production efficiency, and is also a key strategy in the effort to improve the microbiological safe status of animal-derived food products (e.g. by poultry, rabbits, ruminants, or pigs). This review presents some of the alternatives currently used in food-producing animals to influence their health in relation to human health.