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

What is the microbe we are dealing with? Irrespective of cholera or anthrax, we want to know the disease causing microorganism as quickly as possible since prompt identification of the etiology organism would help control disease spread, and save lives through provision of appropriate care and medicine. But despite the promulgation of rapid microbe identification tools (such as 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 environment samples. Mass spectrometry-based methods, however, have increasingly complemented traditional approaches in clinical and research laboratories - but they rarely feature in undergraduate curricula. Motivated by the desire to bridge the curriculum gap, I developed an inquiry-based laboratory exercise for introducing students to the operating principles and methodology of mass spectrometry enabled microbe identification. By requiring students to identify microbes in environment water samples (a real life problem with unknown answers), the exercise piqued the students’ interest in learning, while helping stir their curiosity in science 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 education research and expands on the discussion of concepts underlying matrix assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) microbe identification. Specifically, the article discusses the relative advantages and disadvantages of the pattern recognition and proteome database search approaches for analyzing mass spectra data. In addition, the effect of different sample preparation protocols on identification accuracy is also discussed in detail. Finally, the pedagogy utility of field and inquiry-based education 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 is published in the Journal of Microbiology and Biology Education, Vol. 14, No. 1, pp. 103-106, and is available as an open access article at http://www.asmscience.org/content/journal/jmbe/10.1128/jmbe.v14i1.494