There're CRISPRs in My Yogurt: A Discovery-Based CURE at the Intersection of Industrial Food Production and the Human Microbiome.

Katherine L Petrie

doi:10.3389/fmicb.2020.578737

Abstract

Support for undergraduate laboratory education based on a CURE (Course-based Undergraduate Research Experience) model is more widespread than ever. By giving students the opportunity to conduct genuine research in laboratory courses they are required to take, CUREs can expose more students to scientific practice and have the potential to make science more inclusive, especially when research topics have direct impact on students’ lives. Here, I present a new microbiology CURE module where students explore the real-world intersection between industrial food production and the human microbiome. In this module, students sequence CRISPR arrays in the genomes of lactic acid bacteria they isolate from yogurt. Natural CRISPRs (Clustered Regularly Interspaced Short Palindromic Repeats) act as the bacterial immune system. When a bacterial cell survives viral infection, it can incorporate a bit of that virus’s DNA into its own genome, and produce small RNA guides that surveil the cell, ready to deploy virus-destroying enzymes if matching DNA from a fresh viral infection is detected. This viral immunity is of particular interest in the fermentation industry, since viral infection can destroy stocks of starter cultures and batches of product. Commercial producers of lactic acid bacteria for yogurt production often endeavor to produce strains with large CRISPR arrays and robust immunities. With this context, students are given the task of cataloging the viral immunities found in both commercial and traditionally produced yogurt, and exploring their potential impact on human health. Wet-lab practices (strain isolation, PCR, and Sanger sequencing) are combined with bioinformatic and literature sleuthing to identify the viruses to which bacteria are immune and explore whether consumption of these strains could impact human health via interactions with the human microbiome. Here, a detailed implementation of the module is presented with guides for educators and students.

Highlights

Educational ContextIn the past decade or two there has a been an increasing call to make the science students learn in laboratory courses more reflective of the way science is conducted (American Association for the Advancement of Science [AAAS], 2011)
This paper presents a CURE module, “There’re CRISPRs in my Yogurt” that could be incorporated into an undergraduate microbiology laboratory course
Implementation of Module in Undergraduate Lab Course. This module was incorporated into a redesigned upper-level Microbiology Laboratory course taken primarily by juniors and seniors

Summary

Introduction

Educational ContextIn the past decade or two there has a been an increasing call to make the science students learn in laboratory courses more reflective of the way science is conducted (American Association for the Advancement of Science [AAAS], 2011). One way to do this is through research projects that are open-ended and more authentic than standardized cookbook style activities In these projects, do the students not know what the results might be, but neither does the instructor, nor the scientific community at large. CURES can make science more inclusive by providing research opportunities for students who, due to economic hardship or other systemic barriers, are unable to obtain a traditional, apprenticed, extracurricular research position in a laboratory (Bangera and Brownell, 2017). Because of these potential benefits, CUREs have become increasingly widespread. These studies aim to identify which components of CUREs make them beneficial to students, and provide a framework for how CUREs may benefit students by increasing persistence in science

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