Teaching Microbiome Analysis: From Design to Computation Through Inquiry

Frontiers in Microbiology
Gail L Rosen, Penny Hammrich

Abstract

In this article, we present our three-class course sequence to educate students about microbiome analysis and metagenomics through experiential learning by taking them from inquiry to analysis of the microbiome: Molecular Ecology Lab, Bioinformatics, and Computational Microbiome Analysis. Students developed hypotheses, designed lab experiments, sequenced the DNA from microbiomes, learned basic python/R scripting, became proficient in at least one microbiome analysis software, and were able to analyze data generated from the microbiome experiments. While over 150 students (graduate and undergraduate) were impacted by the development of the series of courses, our assessment was only on undergraduate learning, where 45 students enrolled in at least one of the three courses and 4 students took all three. Students gained skills in bioinformatics through the courses, and several positive comments were received through surveys and private correspondence. Through a summative assessment, general trends show that students became more proficient in comparative genomic techniques and had positive attitudes toward their abilities to bridge biology and bioinformatics. While most students took individual or 2 of the courses, we show that pre-...Continue Reading

References

Dec 8, 2005·Applied and Environmental Microbiology·Catherine Lozupone, Rob Knight
Mar 9, 2012·Methods in Molecular Biology·Daniel H Huson, Suparna Mitra
Jun 13, 2012·Nature Methods·Nicola SegataCurtis Huttenhower
May 20, 2014·Journal of Microbiology & Biology Education·Theodore R Muth, Catherine M McEntee
May 8, 2015·Journal of Microbiology & Biology Education·Brian B GibbensJanet L Schottel
Apr 14, 2016·Nature Communications·Peter MenzelAnders Krogh
Sep 2, 2017·Journal of Microbiology & Biology Education·Thomas B LentzCarlos C Goller
Jul 27, 2015·Journal of Circulating Biomarkers·Kimberly FalanaWinston Patrick Kuo
Nov 20, 2018·American Journal of Botany·J Phil Gibson, Teresa Mourad
Jan 1, 2019·Journal of Microbiology & Biology Education·Gili Marbach-Ad, Jack Marr
Jul 26, 2019·Nature Biotechnology·Evan BolyenJ Gregory Caporaso
Nov 30, 2019·Genome Biology·Derrick E WoodBen Langmead

❮ Previous
Next ❯

Methods Mentioned

BETA
PCR
electrophoresis
amplicon sequencing
PCA

Software Mentioned

NIBLSE
Github
Metaspades
Microbiome Analysis
Biopython
BLAST
shell
Metaphlan2
NCBI
UD

Related Concepts

Related Feeds

Bioinformatics in Biomedicine

Bioinformatics in biomedicine incorporates computer science, biology, chemistry, medicine, mathematics and statistics. Discover the latest research on bioinformatics in biomedicine here.

Related Papers

Frontiers in Microbiology
Theodore R Muth, Avrom J Caplan
European Journal of Dental Education : Official Journal of the Association for Dental Education in Europe
C CoyleR Freeman
© 2021 Meta ULC. All rights reserved