Identifying microbes via mass spectrometry: An inquiry-based educational tool

Abstract

Rapid detection and identification of microorganisms is important for clinical diagnostics and quality control in the food industry. Current methods for identifying microbes rely on cell cultivation or, molecular nucleic acid analysis (16S rRNA sequencing). Besides long time-toresult of a few days, culture-based methods are also prone to false-negatives since 99% of all known microorganisms have not been cultured under laboratory conditions. Although 16S rRNA analysis is culture-independent and thus more expeditious than cell culture bias associated with primer selection may also negatively impact on identification accuracy. In contrast, matrixassisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has emerged, over the past decade, as a rapid and relatively low-cost microbial identification tool. Specifically, microbes are identified either by matching the mass spectrum of an unknown microorganism with those present in a reference database or, via a proteome database search approach which relates individual mass peaks to biomarker proteins exhibiting speciesor strainspecific signatures. Though commercialized, MALDI-TOF MS microbial typing has received less attention in undergraduate life sciences curriculum relative to cultureand 16S rRNA-based techniques. Thus, a simple inquiry-based laboratory exercise for teaching microbial identification via a combined MALDI-TOF MS and proteome database search approach was developed to help bridge the curriculum gap. Specifically, students were exposed to a suite of activities ranging from sample collection to cell culture and mass spectrometric analysis, followed by bioinformatics analysis of mass spectra data, during identification of unknown microorganisms in an environmental water sample. Collectively, by encouraging students to use deductive and inductive thinking skills in solving a real-life problem with unknown answers, the educational module helped ignite their inquiring minds in addition to teaching leading-edge mass spectrometry-based microbial identification techniques and concepts. The article describing the work, “Teaching Microbial Identification with Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) and Bioinformatics Tools,” has been published in the Journal of Microbiology and Biology Education, Vol. 14, No. 1, pp. 103-106, and, together with the supplementary material, is available at http://jmbe.asm.org/index.php/jmbe/article/view/494 as an open-access article.