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Yeast biomass as well as biomass enriched with trace minerals have been demonstrated to be useful in improving animal health and growth performance. In this work, process for the production of Saccharomyces cerevisiae biomass enriched with manganese, a microelement with antioxidant properties in the form of high bioavailable Mn-protein complex, has been studied. The influences of media composition, Mn2+ concentration and Mn salt were investigated in shaken cultures. The change of biomass and ethanol yields was not observed in molasses media with addition of Mn, while in sucrose media the decrease was observed at Mn2+ concentrations higher than 0.8 mM (added as sulphate) and 0.2 mM (added as chloride). It was established that aeration mode (anaerobic, shaken flask or aerated culture) influences amount and dynamic of Mn incorporation into the yeast biomass, and that this incorporation was S. cerevisiae strain dependent. The Fourier transform infrared (FTIR) spectrophotometry on blank and Mn loaded biomass suggested that carboxyl groups, N-H groups of secondary amide, and sulfonate groups are involved in mechanism of manganese binding.