Strategies have been developing to treat and prevent physiological and metabolic disorders by use of genetically modified microorganisms as a nutritional supplement. The present review focuses on the recombinant probiotics of Saccharomyces cerevisiae var. boulardii, which plays a major role in human gastric conditions like high temperature, low pH, mixtures of organic acids, maximum bile, high concentrations of gastric juices, and anaerobic conditions. Along with this tolerance, recombinant probiotics can absorb zinc sulfate, enhance vitamin B6 productivity, convert CIN into COU, and resist 5-fluoroorotic acid, uracil, and uridine by the expression of desired enzymes, whereas in the wild type it is not observed. Probiotic Saccharomyces cerevisiae, in addition to its probiotic activity, has been showing a few therapeutic applications in humans, like enhanced antimicrobial and prophylactic activity by point mutations and by the expression of serum albumin, insulin, transferrin, hirudin, urate oxidase enzymes, and GM-CSF. After genetic manipulation in the probiotic Saccharomyces cerevisiae, it enhanced immunological effects in the host for the expressed antigens like β-lactamase, S. aureus nuclease A, TSST-I, the A-chain of Shiga-like toxin, heat-labile enterotoxin, cholera toxin-B, ASPs, Bloom and Werner’s syndrome, HBsAg, HCV, PEDV, cervical cancer, CD4+, and CD8+. Similar findings were noted with recombinant probiotic Saccharomyces cerevisiae in veterinary applications like phytate degradation, bovine interferon, growth hormone expression, and immunization to IBD, porcine pleuropneumonia, PPV, ETEC antigens, etc. In the fishery field, recombinant Saccharomyces cerevisiae is used as a probiotic for nutritional supplements, for the expression of growth hormone, for immunization to Vibrio harveyi, and for pancreatic necrosis. Slight modifications in the gene sequence and by expression of specific genes in beneficial organisms like the probiotic Saccharomyces cerevisiae may result in reduction of metabolic disorders in the living forms.