Fiber Force: A Fiber Diet Intervention in an Advanced Course-Based Undergraduate Research Experience (CURE) Course

Abstract

Course-based undergraduate research experiences (CUREs) are an effective way to introduce students to contemporary scientific research. Research experiences have been shown to promote critical thinking, improve understanding and proper use of the scientific method, and help students learn practical skills including writing and oral communication. We aimed to improve scientific training by engaging students enrolled in an upper division elective course in a human microbiome CURE. The "Fiber Force" course is aimed at studying the effect of a wholesome high-fiber diet (40 to 50 g/day for two weeks) on the students' gut microbiomes. Enrolled students participated in a noninvasive diet intervention, designed health surveys, tested hypotheses on the effect of a diet intervention on the gut microbiome, and analyzed their own samples (as anonymized aggregates). The course involved learning laboratory techniques (e.g., DNA extraction, PCR, and 16S sequencing) and the incorporation of computational techniques to analyze microbiome data with QIIME2 and within the R software environment. In addition, the learning objectives focused on effective student performance in writing, data analysis, and oral communication. Enrolled students showed high performance grades on writing, data analysis and oral communication assignments. Pre-and post-course surveys indicate that the students found the experience favorable, increased their interest in science, and heightened awareness of their diet habits. Fiber Force constitutes a validated case of a research experience on microbiology with the capacity to improve research training and promote healthy dietary habits.

High fiber, whole foods dietary intervention alters the human gut microbiome but not fecal short-chain fatty acids

“…Twenty-six individuals participated in a CURE course at UC Irvine, designed to tandemly investigate pedagogical methods (25) and the role of fiber on the microbiome. We collected nutritional data from all 26 individuals who initially began the intervention, over three weeks (one week prior to, and two during, the dietary intervention) ( Figure 1A ).…”

“…Subjects provided three fecal samples from three days during week three, concluding the intervention period. As part of the CURE course, students were educated on human health, dietary information on high-fiber meals, the human gut microbiome, and the quantitative methods for microbiome analyses (from DNA extraction and library preparation to metagenome and statistical analyses), as previously described (25).…”

“…and 3) if we observe compositional shifts in the microbiome, do these correspond with metabolic changes in the production of short-chain fatty acids? To address these questions, we developed and employed a course-based undergraduate research experience (CURE) at UC Irvine to assess individual responses to a high-fiber diet (25). Integrating authentic research experiences within lab courses in order to facilitate a deeper understanding of academic and industrial research continues to be a priority for both national education reform and the American Society for Microbiology (25–28).…”

“…To address these questions, we developed and employed a course-based undergraduate research experience (CURE) at UC Irvine to assess individual responses to a high-fiber diet (25). Integrating authentic research experiences within lab courses in order to facilitate a deeper understanding of academic and industrial research continues to be a priority for both national education reform and the American Society for Microbiology (25–28). During the intervention, participants were given ten meals each week from a food service that specializes in providing high fiber, unprocessed meals.…”

PUMAA: A Platform for Accessible Microbiome Analysis in the Undergraduate Classroom

“…Microbiome research using marker gene metabarcoding is an attractive direction for CUREs, as sample collection is relatively straightforward and advances in sequencing technologies and reduced cost have made the acquisition of marker gene microbiome data easier than ever ( Clooney et al, 2016 ; Jovel et al, 2016 ). The large microbiome datasets using a combination of marker genes targeting bacteria and archaea (16S), eukaryotes (18S), and fungi (ITS) give students an opportunity to ask a variety of questions ranging from the composition of their own oral microbiome to plant–microbe interactions ( Rosenwald et al, 2012 ; Sanders and Hirsch, 2014 ; Wang et al, 2015 ; Weber et al, 2018 ; Parks et al, 2020 ; Sewall et al, 2020 ).…”