2023 ASEE Annual Conference & Exposition

Advances in Graduate Training in Integrative Bioinformatics for Investigating and Engineering Microbiomes (IBIEM)

Presented at Design in Engineering Education Division (DEED) Technical Session 11

Innovations by engineers and physical scientists working at the frontiers of microbiome engineering and discovery requires in-depth understanding of microbiome systems with parallel skills to apply bioinformatics and biostatistics. Despite the importance of integrating bioinformatics and biology into graduate student training in fields outside traditional biological sciences, academic institutions remain challenged with including these disciplines across departmental boundaries. Furthermore, it is critical for students in engineering, bioinformatics, and biostatistics to understand fundamentals behind the biological systems they model, and for biology students to gain competencies to apply bioinformatics and biostatistics in quantitative biology arenas. To address these needs, the Integrative Bioinformatics for Investigating and Engineering Microbiomes (IBIEM) graduate training partnership between Duke University and North Carolina Agricultural and Technical State University was developed and funded by the National Science Foundation Research Traineeship (NRT) program. IBIEM’s goals include training interdisciplinary groups of students to: (a) transform conceptualization and develop skills for application of quantitative biology in microbiome areas; b) perform cutting edge research requiring interdisciplinary team skills; and to (b) communicate their research across disciplinary barriers and to diverse audiences. The pedagogical framework adapted to foster trainee engagement is learner-centered teaching which emphasizes the importance of self-directed learning with parallel ongoing assessment to optimize student outcomes. Since IBIEM trainee goals as well as entry-level knowledge and skills across disciplines varied greatly, program implementation was found to be challenging and required rigorous evaluation and refinements for effective training across disciplines and skill levels. A comprehensive program evaluation over five years found that the strongest learning and skills outcomes were linked to several “best practices”. Early provision of depth in fundamentals in R studio and Git Hub was found to be critical to “jump start” students without coding backgrounds. Addition of an overview of microbiome experimental design and analysis added important context as to how and where in the research process informatics fits into design progression and was highly motivating to students. Course modality was found to impact trainee outcomes with in-person classes that included hands-on practice and feedback showing greater improvements in training outcomes over hybrid, flipped and virtual course modalities. Furthermore, introduction of low, medium, and high level “challenges” along with in-person tutoring was found to be impactful in building a common foundation to span expertise levels and for engaging students across entry and advanced levels. Training impacts peaked during year four with cumulative implementation of revised strategies. Innovative training revisions and inclusion of critical elements was strongly linked to program satisfaction and ratings of advances in technical, professional and career skills as well as post-training carry over into trainees’ own research and leadership in their labs and careers. Furthermore, this training collaboration and partnership provided the foundation and training model for a newly funded NSF Engineering Research Center for Precision Microbiome Engineering (PreMiEr) for work in the critical area of engineering the microbiome in built environments.

Authors

Dr. Glenda T. Kelly Duke University [biography]

Glenda Kelly is Director of Evaluation and Assessment for the National Science Foundation Engineering Research Center for Precision Microbiome Engineering (PreMiEr), Civil and Environmental Engineering, Duke University. She previously served as Associate Director for Assessment and Outreach for the Center for the Environmental Implications of NanoTechnology (CEINT), Duke. For both Centers she designed the overall evaluation plan and collaborated with leadership to define measurable goals related to training, diversity, inclusion and synergy across partners and research thrusts as well as impacts on institutional infrastructure. Since 2000, Dr. Kelly has worked in the area of STEM program development and evaluation for international research centers, NRTs, PIREs, REUs, GK-12 and faculty advancement. She served as evaluator for the Integrative Bioinformatics for Investigating and Engineering Microbiomes (IBIEM) NSF Research Traineeship (NRT) program (2015-21) and was instrumental in providing feedback to optimize this training model. She has chaired evaluation sessions at NSF NRT and other NSF meetings. She has special interest in developing training to optimally engage students under-represented in STEM, across disciplines and with differing entry level skill sets. Dr. Kelly served as a founding member of the Pratt School of Engineering's Diversity and Inclusion Committee and earned her M.A. and Ph.D. degrees from Duke University with a concentration in development of assessment tools.
Dr. Joshua Granek Duke University [biography]

Josh Granek is an Assistant Professor of Biostatistics and Bioinformatics at Duke University. He joined the Duke Faculty in 2012 after postdoctoral positions at Duke and the National Evolutionary Synthesis Center, receiving his Ph.D. from Johns Hopkins University, and his Sc.B. from Brown University. He is Education Co-Director for the National Science Foundation Engineering Research Center for Precision Microbiome Engineering (PreMiEr) and Associate Director for Microbiome and Genomics of the Duke Center for AIDS Research Quantitative Sciences Core. He was previously co-PI and Instructor for IBIEM (Integrative Bioinformatics for Investigating and Engineering Microbiomes), a joint graduate training program between Duke and North Carolina A&T State University (2015-2021). Dr. Granek's research is primarily in Bioinformatics with focuses in microbiome, microbial genomics, cancer genomics and immunoinformatics.
Dr. Claudia K. Gunsch Duke University [biography]

Claudia Gunsch is a Professor of Civil and Environmental Engineering at Duke University and holds secondary appointments in the Nicholas School of the Environment and the Department of Biomedical Engineering. She joined the Duke Faculty in 2004 after obtaining her PhD from the University of Texas at Austin, her MS from Clemson University and her BS from Purdue University. Currently, she serves as the Director for the National Science Foundation Engineering Research Center for Precision Microbiome Engineering (PreMiEr). Previous leadership roles include serving as the Director of IBIEM (Integrative Bioinformatics for Investigating and Engineering Microbiomes), a joint graduate training program between Duke and North Carolina A&T State University (2015-2021). Dr. Gunsch’s research bridges environmental engineering and molecular biotechnology. Current research foci include developing microbiome engineering approaches for the built environment and bioremediation, investigating the ecological impacts of emerging contaminants on environmental microbiomes, studying microbial evolution following exposure to anthropogenic contaminants and developing innovative water treatment technologies. Dr. Gunsch was named ASCE Environmental & Water Resources Institute Fellow in 2022. She currently serves as Editor in Chief for Biodegradation and is a member of the Editorial Board for npj Clean Water and Industrial Biotechnology.
Dr. Joseph L. Graves Jr. North Carolina A&T State University [biography]

Joseph L Graves, Jr. received his Ph.D. in Environmental, Evolutionary and Systematic Biology from Wayne State University in 1988. In 1994 he was elected a Fellow of the American Association for the Advancement of Science (AAAS) and in 2012 chosen as one of the “Sensational Sixty” commemorating 60 years of the NSF Graduate Research Fellowship Award. In 2017, he was listed as an “Outstanding Graduates” in Biology at Oberlin College; and named “Innovator of the Year” in US Black Engineer Magazine. He was named “Senior Researcher of the Year” at North Carolina A&T State University in 2023. He leads programs addressing underrepresentation of minorities in science. His research in the evolutionary genomics of adaptation shapes our understanding of biological aging and bacterial responses to nanomaterials. He is presently Associate Director/co-PI of the Precision Microbiome Engineering (PreMiEr) Engineering Research Center of Excellence (Gen-4 ERC) funded by the National Science Foundation (2022—2027). He also was co-PI for the IBIEM (Integrative Bioinformatics for Investigating and Engineering Microbiomes), a joint graduate training program between Duke and North Carolina A&T State University (2015-2021). His five books include: A Voice in the Wilderness (New York: Basic Books), 2022; with Alan Goodman, Racism, Not Race (Columbia University Press), 2022; Principles and Applications of Antimicrobial Nanomaterials, (Amsterdam NE: Elsevier), 2021; The Emperor's New Clothes, (Rutgers University Press), 2005 and The Race Myth (Dutton Press), 2005.
Dr. David Singleton Duke University [biography]

David Singleton is an Executive in Residence in the Department of Civil and Environmental Engineering in Duke University's Pratt School of Engineering. He also hold an adjunct faculty appointment in the Department of Environmental Sciences and Engineering at the University of North Carolina at Chapel Hill in the Gillings School of Global Public Health. He holds a PhD in Microbiology from the University of Georgia. His prior research focused on the bioremediation of contaminated soils and the cultivation and description of novel microorganisms. Currently, he serves as the Administrative Director for the NSF Engineering Research Center for Precision Microbiome Engineering at Duke University.

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