Des Moines University Doctor of Osteopathy (D.O.) students, Calvin Fung (D.O.’22), Mathew Rusling (D.O.’21), Charles Love (D.O.’24), Anisha Karim (D.O.’24), Christian Bongiorno (D.O.’24), and faculty mentor, Lillian Yuan, Professor of Physiology and Pharmacology, have published “Automation of QIIME2 Metagenomic Analysis Platform,” in the journal Current Protocols.
QIIME is a widely used open-source bioinformatics pipeline for performing microbiome analysis and has been applied to studies based on billions of DNA sequences from tens of thousands of samples. The latest version of this tool, QIIME2, has a steep learning curve for new and experienced users thereby increasing the risk of user error and inefficient result reproducibility. To address this weakness in QIIME2 and with funding from the Des Moines University’s Iowa Osteopathic Education and Research (IOER) Grant, Dr. Yuan and her team of student researchers, developed a chain of automation scripts that reduces the risk of error, number of keystrokes, and time spent on metagenomic analysis while increasing accessibility for novice users. The team’s contribution has made QIME2 a user-friendlier product that will better integrate new users into the field of metagenomics and enhance collaboration.
Remarkably, all the article’s authors except Dr. Yuan (the senior author) are D.O. students ranging from the first to fourth years. This is truly a great achievement given this published work was conducted during the COVID pandemic shutdown of 2020 when these students were taking online lectures, doing clinical rotations, and dealing with all other challenges brought about by the pandemic.
Dr. Henry, Chair of the Physiology and Pharmacology department, noted that this publication is exactly the type of experience students are looking for and positions them for a competitive edge for residency programs.