The present invention relates to an improved method for the fermentative production of stable isotope labeled metabolites in a microorganism, particularly stable isotope labeled amino acids, stable isotope labeled monosaccharides, stable isotope labeled lipids, or mixtures thereof, wherein the stable isotope labeled metabolites are isolated from the cell wall and/or the cell membrane of the microorganism. Specifically, the invention provides a method of preparing one or more stable isotope labeled metabolites selected from stable isotope labeled amino acids, stable isotope labeled monosaccharides, stable isotope labeled lipids, and mixtures thereof, the method comprising: cultivating a microorganism in the presence of a stable isotope labeled nutrient; isolating the cell wall and the cell membrane of the microorganism; and isolating said one or more stable isotope labeled metabolites from the isolated cell wall and/or the isolated cell membrane.
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