ASM's MRA Journal Supports Undergraduate Research

Disclaimer: Dr. Irene Newton is EiC of ASM's Microbiology Resource Announcements and Catherine Putonti is a Senior Editor.

Undergraduate research changed my life. Truly. Along with many thousands of other undergraduate students, I started my career really thinking I was going to be an MD. That career path appealed for many reasons - my immigrant family understood it and approved, it was prestigious, and it meant my life was planned out for the next decade. But one semester of research with my undergraduate mentor was enough to get me hooked. I was privileged to have the opportunity to do one-on-one research at a small liberal arts institution but not all of our students have that opportunity. I now teach at one of the "Big 10" - with over 45,000 undergrads on campus there is no way we can provide all of them the research experience I had. But we can and are trying to integrate true scientific research into our undergraduate classes. Some good examples of this are the FIRE program at UTAustin, which we are emulating at IU with the ASURE program. These programs put introductory science in context, allowing young students the opportunity to really explore a scientific system or question. At Loyola, Dr. Catherine Putonti offers an undergraduate course called "Bacterial Genomics" that brings in 24 students a year to take a project from bacterial isolate to draft genome.

"The students use the 16S rRNA gene to confirm identity of the isolates early in the semester - for many of them this is the first time they are really doing PCR and sequencing" - Dr. Putonti

Students in Bacterial Genomics at the bench isolating DNA from their bacterial isolates

The basic plot-arc of the course is this - students work with collaborators in clinical labs to get access to  samples. They re-isolate the microbes on media (learning basic microbiology and sterile technique), they identify them by 16S rRNA sequencing, and they sequence, assemble, and annotate the genome. Guest lectures from clinical collaborators contextualize the organisms and help provide more background for the students.  "The goal of the course is to act as a teaser for bioinformatics research" for the students, says Putonti. And it works. Last year alone, two students switched to a bioinformatics major. 

"Overall, this class has increased my interest in both microbiology and genomics. I had the unique opportunity to take this course while simultaneously taking microbiology. For this reason, I was able to learn about lab techniques and apply them in both microbiology lab and this class. I gained a greater appreciation for microbiology as I was able to immerse myself into such topics and perform such techniques firsthand. The ability to extract such valuable information from the genome of different bacteria continues to amaze me. Dr. Putonti has instilled in me a fire to continue to explore these databases and hopefully apply them in future research." Erika Balce - student in Bacterial Genomics

A student in Dr. Putonti's class presents her research on antibiotic resistance based on hypotheses generated from sequencing the isolate

"But as we’ve been studying these genomes, in most cases, we are the major contributor to the genomic data that’s out there, an amazing accomplishment for undergraduate researchers. We’ve made interesting discoveries along the way, which has led to some students taking the project beyond the class." says Dr. Putonti. Indeed, beginning the first year the class was run, several students have followed up by developing hypotheses based on the genomic data and testing them in the lab. In the end, students in Dr. Putonti's class have used ASM's Microbiology Resource Announcements (MRA) to make their genomes, and the protocols used to generate them, available to the community. A total of 30 MRA manuscripts have now been published from Dr. Putonti's class and include everything from Lactobacillus to Enterobacter genomes. 

Dr. Putonti says that the MRA format is particularly good for this type of course. "I provide the students 3 examples of good MRA papers and then they have to identify common elements in the papers to try and figure out the requirements." The students have no problem figuring out common elements across MRA manuscripts and the length is not overwhelming, which is good for an undergraduate research course. "I also give students examples of bad MRAs to get them to find what details are missing." says Dr. Putonti. Overall, MRA's formulaic author instruction list and detailed requirements make an introduction to scientific writing easy for undergraduates, the majority of which have never written a paper before.

"Having the opportunity to write scientific literature based off of a genome annotation really opens a lot of doors to potential research opportunities.  From studying phages present within a genome to testing a genome's antibiotic resistance, a lot of knowledge can be obtained.  I am thankful for the opportunity this course has given me to have a hands on experience in the field of microbiology and genomics." - Noreen Gallian, student in Bacterial Genomics 

Do you have an undergraduate course using project-based learning? Are you interested in having your students publish their announcements in MRA? ASM's MRA is proud to support undergraduate researchers and their first author publications. Please reach out to the EiC!