Breaking Barriers with Bread: Using the Sourdough Starter Microbiome to Teach High-Throughput Sequencing Techniques

Benjamin H Holt; Alison Buchan; Jennifer M DeBruyn; Heidi Goodrich-Blair; Elizabeth McPherson; Veronica A Brown

doi:10.1128/jmbe.00306-21

Breaking Barriers with Bread: Using the Sourdough Starter Microbiome to Teach High-Throughput Sequencing Techniques

J Microbiol Biol Educ. 2022 May 16;23(2):e00306-21. doi: 10.1128/jmbe.00306-21. eCollection 2022 Aug.

Authors

Benjamin H Holt¹, Alison Buchan², Jennifer M DeBruyn^{2

3}, Heidi Goodrich-Blair², Elizabeth McPherson², Veronica A Brown^{2

4}

Affiliations

¹ Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee, USA.
² Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA.
³ Department of Biosystems Engineering & Soil Science, University of Tennessee, Knoxville, Tennessee, USA.
⁴ Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA.

Abstract

Widespread usage of high-throughput sequencing (HTS) in the LIFE SCIENCES has produced a demand for undergraduate and graduate institutions to offer classes exposing students to all aspects of HTS (sample acquisition, laboratory work, sequencing technologies, bioinformatics, and statistical analyses). Despite the increase in demand, many challenges exist for these types of classes. We advocate for the usage of the sourdough starter microbiome for implementing meta-amplicon sequencing. The relatively small community, dominated by a few taxa, enables potential contaminants to be easily identified, while between-sample differences can be quickly statistically assessed. Finally, bioinformatic pipelines and statistical analyses can be carried out on personal student laptops or in a teaching computer lab. In two semesters adopting this system, 12 of 14 students were able to effectively capture the sourdough starter microbiome, using the instructor's paired sample as reference.

Keywords: high-throughput sequencing; microbiome; sourdough.