A method for enzyme quenching in microbial metabolome analysis successfully applied to gram-positive and gram-negative bacteria and yeast

Although microbial metabolome analysis has now become a widely used method, no generally applicable quenching method has been published so far. Either the methods were established for only one defined organism or the metabolite coverage was quite low. In the current work, a novel, reliable, and robust quenching method for different types of organisms is described. Compared with the commonly used quenching procedure with 60% methanol (−50 °C), we obtained improved results for three examined organisms with different cell wall and membrane structures using a 40% ethanol/0.8% sodium chloride solution (−20 °C). Increased metabolite levels were achieved for 60–80% of all identified compounds. Moreover, the estimated standard error of the relative concentrations of 120–160 different substances was only 14 ± 4% compared with 17 ± 3% in unquenched samples and 24 ± 7% in samples quenched with methanol for the different tested organisms.