The purpose of this semester-long Lesson is to give students an authentic, course-based undergraduate research experience during which they learn basic and advanced microbiological and molecular biology techniques. This project begins with the isolation of a suspected Streptomyces bacterium from a soil sample and concludes with its identification. Students collect data, regarding colony and cell morphology, biochemical characteristics, the production of secondary metabolites, and employs the PCR using custom-designed primers to the Streptomyces 16s rRNA gene. The project culminates with the identification of their soil isolate using the National Center for Biotechnology Information (NCBI) web site to perform nucleotide blasts. The blastn program provides the final piece of evidence used to confirm, or not, the identification of their isolate as a Streptomyces from 16s rRNA gene sequence data, hence the title “From Dirt to Streptomyces DNA. In addition, the Lesson focuses on the Streptomyces bacteria to address several ASM aligned goals and objectives. These include prokaryotic growth phases and ways in which interactions of microorganisms among themselves and with their environment is determined by their metabolic abilities.  In addition, this Lesson illustrates how microbial metabolism is important to a relevant societal issue, the need for new antibiotic discovery particularly given the rise of antibiotic resistance strains of clinically relevant bacteria. It also illustrates the microbial diversity of soil and the developmental/physiological strategies employed in such a competitive environment. This Lesson hopes to impart both the thrill and challenges associated with scientific discovery.

Primary image: Photomicrograph of Streptomyces colonies growing on ISP 2 agar. The Streptomyces are student isolates showing stages of morphological development. Photomicrograph by Marc A. Brodkin.

The students will analyze the human gut and vaginal microbiomes in healthy and diseased states using diversity of bacteria as determined by 16SrRNA sequence.

Creating a hands-on lab that conveys important information while simultaneously allowing for student autonomy can be difficult. This is particularly true for the field of microbiology, in which labs often rely on “recipe-style” instructions and materials that can be difficult to scale up for larger class sizes. For these reasons, microbiology concepts are often left out of introductory biology labs, the ramifications of which have been made apparent during the recent COVID-19 virus pandemic. Fundamental microbiology concepts, e.g., the prevention of communicable diseases, are important to teach in introductory biology classrooms – often a student's only exposure to biology in their academic careers – in order to create a healthier community as a whole. Therefore, this general biology lab introduces an active-learning microbiology lab that teaches students about the microbial world. Students are first introduced to the three major types of symbioses and apply these concepts to microbial organisms on a symbiotic continuum. Next, the students are given examples of mutualistic bacteria, i.e., the human microbiome, through a mini lecture prepared by the instructor. The students are then introduced to examples of parasitic/pathogenic microbes that can interfere with human health and cause relatable diseases (e.g., diarrhea, STDs, and athlete’s foot). Students then apply this information through a short matching game before learning common practices used to prevent the spread of these pathogens, including an active learning exercise and video on how to wash their hands like healthcare professionals. Finally, students are asked to generate their own questions about microbes before working through a handout that guides the students through using the scientific method to address their questions. This exercise thus provides students with the autonomy to ask their own questions about microbes, design their own experiments, prepare growth media their own way, and present their findings in a way that is both scalable for large class sizes and reduces the burden of lab prep common for microbiology labs. 

Primary image: Microbes sampled from the iPhone of a curious individual. Fungal colonies can be seen as fuzzy, white or colorful mounds while bacteria appear as opaque, smooth streaks on the media.

This interactive assignment engages students in a hands-on exploration of microbial diversity and the importance of microbes in ecosystems. Designed for General Biology II and Introduction to Microbiology courses, the activity accommodates class sizes of 10-30 students. Within a 55-minute class period, students work in groups to research, analyze, and present various microorganisms. This guide includes detailed steps for instructors, a student worksheet, a PowerPoint presentation with microbial images, and quizzes to assess student learning.