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These inventors used a combination of rational design and unbiased transcriptomics to develop a chemically defined growth media for Pichia pastoris. Complete medium increases growth rate by supplying organisms with important metabolic intermediates so that the organisms do not need to use energy to synthesize their own. The inventors therefore determined the rate-limiting metabolic intermediates for Pichia growth and designed growth media that provides these nutrients. This medium, called rich defined medium (RDM), contains defined concentrations of glutamine, arginine, asparagine, vitamins, and fatty acids. Growth in RDM media increases the growth rate of Pichia to nearly the same rate as complete medium. Strikingly, RDM also led to substantial improvements in protein expression, and Pichia grown in RDM were shown to produce more heterologous protein per cell than those grown in complete media.