Sulfite plays an important role in beer flavor stability. Although breeding of bottom-fermenting Saccharomyces strains that produce high levels of SO 2 is desirable, it is complicated by the fact that undesirable H 2 S is produced as an intermediate in the same pathway. Here, we report the development of a high-level SO 2 -producing bottom-fermenting yeast strain by integrated metabolome and transcriptome analysis. This analysis revealed that O-acetylhomoserine (OAH) is the rate-limiting factor for the production of SO 2 and H 2 S. Appropriate genetic modifications were then introduced into a prototype strain to increase metabolic fluxes from aspartate to OAH and from sulfate to SO 2 , resulting in high SO 2 and low H 2 S production. Spontaneous mutants of an industrial strain that were resistant to both methionine and threonine analogs were then analyzed for similar metabolic fluxes. One promising mutant produced much higher levels of SO 2 than the parent but produced parental levels of H 2 S.The bottom-fermenting yeast Saccharomyces pastorianus is used to produce beer and has been proposed to be a natural hybrid between Saccharomyces cerevisiae and Saccharomyces bayanus (30). Bottom-fermenting yeasts have two types of genes, one set highly homologous (more than 90% identity) to those of S. cerevisiae and the other less so but highly homologous to S. bayanus (i.e., non-S. cerevisiae [Lg type]) (8,14,27,33). One way in which S. pastorianus differs from baker's yeast (S. cerevisiae) is its tendency to produce higher levels of both sulfite (SO 2 ) and hydrogen sulfide (H 2 S).It is well known that sulfur compounds in beer make significant contributions to flavor and aroma. SO 2 , for example, acts as an antioxidant, which slows the development of oxidation haze and staling of flavors in beer. In contrast, H 2 S has an aroma of rotten eggs and is also a precursor of other compounds with undesirable sensory characteristics. SO 2 and H 2 S are produced by yeast during reductive sulfate assimilation (Fig. 1). Inorganic sulfate is taken up through a sulfate permease and reduced to SO 2 by enzymes encoded by MET3, MET14, and MET16. SO 2 is then reduced to H 2 S by SO 2 reductase encoded by MET5 and MET10 (29). The next intermediate, homocysteine, which is synthesized from H 2 S and O-acetylhomoserine (OAH) by OAH sulfhydrylase encoded by MET17, leads to the formation of cysteine, methionine, and S-adenosylmethionine (SAM). SAM transcriptionally represses all of the genes involved in sulfate assimilation. Park and Bakalinsky previously reported that SSU1 encodes an SO 2 efflux pump that exports intracellular SO 2 through the plasma membrane (18).In the postgenomic era, systematic and high-throughput analyses of mRNA and proteins have become central to recent functional genomics initiatives. Metabolomics entails the analysis of all cellular metabolites and has become a powerful new tool for gaining insight into functional biology. Measurement of numerous metabolites within a cell and tracking concentration changes as a fu...