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The study of the intestinal microbiota is one of the greatest challenges in today’s clinical environment. Thus, probiotics have been established as a focus for its stability, as they play a key role in its regulation. The development of an automated technique that allows the practitioners the smooth search for the optimal probiotic is postulated as the main objective of this study. Despite the existence of previous attempts at applications for this purpose, they have only been carried out for the countries of origin, preventing them from being used in others such as Spain. Therefore, a system has been developed with open, multi-platform, and free technologies, which manages to locate the optimal probiotic for each pathology.