At present, it is relevant to preserve and raise healthy, well-developed newborn animals adapted to new conditions, which form the basis for increasing the yield of animal husbandry. Gastrointestinal diseases cause the main losses of young animals. Acute gastrointestinal diseases of calves, lambs, piglets, and chickens are widespread in Kazakhstan. The study aims to develop a competitive treatment and prophylactic drug composition based on probiotic bacterial strains. Modern certified and standardized biochemical, microbiological, molecular biological studies were considered during the research. The morphological, cultural, and biochemical properties of the cultures were studied according to generally accepted schemes. Standard methods of finding averages and their mean errors were used for the mathematical processing of results. Antibiotics, sulfonamide, and nitrofuran drugs are the most common methods to combat diseases in young animals. However, the use of antibacterial agents often leads to the death of normal microflora, disrupting the microbiocenosis of the gastrointestinal tract, the appearance of microorganisms with resistance to drugs, and a decrease in product quality. In this regard, the direction of biotechnology involved in the development and creation of environmentally friendly microbial preparations with prophylactic effectiveness is very relevant. Data on the prophylactic and therapeutic efficacy of the probiotic strain of Escherichia coli 39-SN are presented.