Faculty Workshops

Faculty workshops on sequencing.

The goal of the workshops is to integrate DNA sequencing, metagenomics, and bioinformatics into undergraduate curricula. We have conducted three Summer Faculty training courses in metagenomics and provided opportunities for faculty from around the USA to sequence environmental microbial communities associated with their research. The microbial communities were from a wide range of ecosystems, including microbes associated with plants, mealworms, diseases of swans, high alpine regions, enrichment cultures from thermophilic environments, infective viruses, soil environments, rivers and ocean trash.
During the workshop, the participants made DNA libraries and conducted the sequencing on the Illumina MiSeq. Once sequenced the participants conducted a range of bioinformatic analysis, including Basespace, FastQC, Prinseq, MG-RAST, Rast, Focus, Superfocus, Stamp, CrAss, SPADES, CheckM, and Anvi’o. At the end of the workshop, the participants left with annotated metagenomes and greater understanding of the DNA sequencing process and bioinformatics.

The participants were from 30 different universities and colleges across the United States, including University of California, Davis; American National University, Torrey Pines; Delaware Valley College, Pennsylvania: Ashland University, Ohio; Hood College, Maryland; Flathead Valley Community College, Montana; Hamilton College, New York; and Alfred College New York and Institutions such as the National Oceanographic and Atmospheric Administration, and United States Geological Society.
The workshops were conducted as part of a grant from the National Institute of Science and the participants are now integrating metagenomics and bioinformatics into classes at their home institutions.