Matters Microbial #119: Investigating Microbial "Dark Matter" December 22, 2025

Today Dr. Julia Willett, Assistant Professor in the Department of Microbiology and Immunology at the University of Minnesota, joins the #QualityQuorum to discuss how to investigate unknown genes found in nearly every bacterial genome. Call it Microbial Dark Matter!

Host: Mark O. Martin

Guest: Julia Willett

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Links for this episode

• Microbial "Dark Matter"—unknown genes in microbial genomes.
• The process of annotation.
• An article about the "Y-ome" or understanding "uncharacterized" genes.
• The smallest independently growing (and engineered) bacterium, JCVI-syn3.0. It still has many "uncharacterized" but necessary genes.
• An essay on Enterococcus faecalis. 
• Diseases caused by Enterococcus.
• The concept of the pathobiont.
• Dr. Arturo Casadevall's thoughts on the term "pathogen."
• The use of transposon mutagenesis to create "knock outs" of bacterial genes.
• Array transposon mutagenesis. Here is an article coauthored by Dr. Willett on that topic.
• The Alpha Fold program for predicting gene function.
• A webinar describing "Microbial Dark Matter" by Dr. Willett.
• Dr. Willett's faculty website.
• Dr. Willett's laboratory website.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com