Testing the "Grandma Hypothesis": Characterizing Skin Microbiome Diversity as a Project-Based Learning Approach to Genomics

Journal of Microbiology & Biology Education
Marcos Pérez-LosadaKeith A Crandall

Abstract

The constantly evolving nature of genomics provides new challenges for students in Public Health as they try to understand how genomic information relates to health and disease. As Public Health curricula attempt to keep pace with the most recent advances in genomics, students should gain experience with analyzing genomic data and applying genomic tools to the study of health-related issues. To advance undergraduate and graduate student education and provide a more comprehensive view of genomics, we developed an educational project including both pedagogic and research components to characterize skin microbial communities (microbiomes) using targeted amplicon sequencing of their genomes (metataxonomy). All students completed the lab procedures, analyzed 16S rRNA genomic data (formative assessments), and wrote a five-page scientific report summarizing and discussing their results (summative assessment). Student grades for the summative assessment ranged from 31.5 to 40 (out of 40) points. They also successfully completed two practicums (problem sets) focused on microbiome sequence data and responded to 12 minute-papers related to genomic topics covered in class. In all these exercises the 2019 students outperformed 2018 students...Continue Reading

References

Dec 23, 2006·Science·David I HanauerGraham F Hatfull
Sep 19, 2008·Nature Chemical Biology·Gabriela C WeaverDonald J Wink
May 8, 2015·Journal of Microbiology & Biology Education·Brian B GibbensJanet L Schottel
Aug 1, 2015·Microbiome·Julian R Marchesi, Jacques Ravel
Apr 20, 2016·Frontiers in Microbiology·Sarah K HiltonKeith A Crandall
May 24, 2016·Nature Methods·Benjamin J CallahanSusan P Holmes
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Jun 7, 2018·Proceedings of the National Academy of Sciences of the United States of America·Ashley A RossJosh D Neufeld
Sep 6, 2018·The Journal of Dermatology·Wanfang ZhaiSen Yang

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Datasets Mentioned

BETA
PRJNA553551

Methods Mentioned

BETA
PCR
amplicon sequencing
electrophoresis

Software Mentioned

R
MicrobiomeAnalyst
dada2
PERMANOVA

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