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The colonization of the digestive tract in animals begins soon after birth or hatching and the normal microbiota changes dramatically during the life of the host. The composition of gastrointestinal microbiota differs between animal species, between individuals within the same species and between the body sites of the host. The gut microbiota is a complex interactive community of organisms and its functions are the result of activities of all microbial components. Together with the host, the microorganisms constitute an ecological system, beneficial for the host, as well as for the microbial species. In principle, the role of gut microbiota in animals is the same as in humans—salvaging energy from the undigested feed components through fermentation, providing the basis for a barrier that prevents pathogenic bacteria from invading the gastrointestinal tract, protective functions together with the gut immune system, a role in metabolism of xenobiotics and contribution to the vitamin and amino acids requirements of the animals (1). Some of these functions are emphasized in farm animals with regard to their environment, character of their feed and the economy of farm animals’ rearing. The composition and metabolism of the gastrointestinal microbiota affects the performance of farm animals in many ways, especially in the young, which are subjected to many stressful conditions. Farm animals can be divided into three main groups according to the degree of development of their gastrointestinal tract and efficacy of feed digestion: (1) omnivorous animals—the feed of plant origin with small content of cellulose and lignin, as well as the feed of animal origin is easily and quickly digested with a help of enzymes produced in the gastrointestinal tract of the animal (pigs), (2) carnivorous animals—under natural conditions they consume mostly feed of animal origin, (3) herbivorous animals—consume feed of plant origin with high content of cellulose and lignin, which the animal is able to digest exclusively through microbial fermentation by its gastrointestinal microbiota (ruminants, horses). Herbivorous animals have some part of their gastrointestinal tract adapted to microbial fermentation. The ruminants are polygastric animals with foregut |
