In microbiology, methyl red is used in the methyl red test (MR test), used to identify bacteria producing stable acids by mechanisms of mixed acid fermentation of glucose (cf. Voges–Proskauer test).

The MR test, the "M" portion of the four IMViC tests, is used to identify enteric bacteria based on their pattern of glucose metabolism. All enterics initially produce pyruvic acid from glucose metabolism. Some enterics subsequently use the mixed acid pathway to metabolize pyruvic acid to other acids, such as lactic, acetic, and formic acids. These bacteria are called methyl-red positive and include Escherichia coli and Proteus vulgaris. Other enterics subsequently use the butylene glycol pathway to metabolize pyruvic acid to neutral end products. These bacteria are called methyl-red-negative and include Serratia marcescens and Enterobacter