Identifying microbes from environmental water samples in a discovery-based learning module

Abstract

What is the microbe that we are dealing with? Whether it is cholera or anthrax, we want to know the disease-causing microorganism as quickly as possible since prompt identification of the causative organism would help control disease spread -and potentially save lives through provision of appropriate care and medication. But despite the advent of rapid microbial identification tools -particularly those based on mass spectrometry -most undergraduate curricula continue to focus on culture-and nucleic acid-based identification techniques since they are widely used for detecting and identifying microbes in clinical and environmental samples. Mass spectrometry-based methods, however, have increasingly complemented traditional approaches in clinical and research laboratories -but are rarely featured in undergraduate curricula. Motivated by the desire to address the curriculum gap, I developed an inquiry-based laboratory exercise for introducing students to the operating principles and methodology of mass spectrometry-based microbial identification. By requiring students to identify microbes in environmental water samples -a real-life problem with unknown answersthe exercise piqued the students' interest in learning, while helping to stir their curiosity through an interesting field activity where they put on a scientist's hat in solving a mystery. This synopsis article summarizes a piece of published educational research and expands on the discussion of concepts underlying matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS)-based microbial identification. For example, the article discusses the relative advantages and disadvantages of the pattern recognition and proteome database search approaches for analyzing mass spectra data. Additionally, the effect of general and tailored sample preparation protocols on identification accuracy is also elaborated. Finally, the pedagogical utility of field-and inquiry-based educational tools is also discussed in greater detail from a post-publication perspective. A full-length synopsis of the work and a structured abstract can be found in the accompanying PDF file, while the original article, "Teaching Microbial Identification with Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) and Bioinformatics Tools," and supplementary material has Abstract Background Rapid detection and identification of microorganisms is important, for example, in clinical diagnostics and quality control in the food industry. Current methods for identifying microbes rely heavily on cell cultivation or, molecular nucleic acid analysis (e.g., 16S rRNA sequencing). Besides long time-to-result of a few days, culture-based methods are also prone to falsenegatives and cultivation-bias 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 assays -bias associated with primer selection reduces identification...