<description>&lt;header class="entry-header clearfix"&gt; &lt;h1 class="entry-title"&gt;Matters Microbial #119: Investigating Microbial "Dark Matter"&lt;/h1&gt; &lt;span class="mini-title"&gt;December 22, 2025&lt;/span&gt;&lt;/header&gt; &lt;div class="entry-content"&gt; &lt;p&gt;&lt;strong&gt;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!&lt;/strong&gt;&lt;/p&gt; &lt;p&gt;Host: &lt;a href= "https://www.pugetsound.edu/directory/mark-martin"&gt;&lt;strong&gt;Mark O. Martin&lt;/strong&gt;&lt;/a&gt;&lt;/p&gt; &lt;p&gt;Guest&lt;strong&gt;&lt;a title="" href= "https://toryhendry.weebly.com/"&gt;: &lt;/a&gt;&lt;/strong&gt;&lt;a title="" href="https://www.willettmicrolab.com/home"&gt;&lt;strong&gt;Julia Willett&lt;/strong&gt;&lt;/a&gt;&lt;/p&gt; &lt;p&gt;Subscribe: &lt;strong&gt;&lt;a href= "https://podcasts.apple.com/us/podcast/matters-microbial/id1701545625"&gt;Apple Podcasts&lt;/a&gt;, &lt;a href= "https://open.spotify.com/show/22BQtkxh56Dy7xRW7yAYvC?si=4c093f07fdaa4e27"&gt;Spotify&lt;/a&gt;&lt;/strong&gt;&lt;/p&gt; &lt;p&gt;Become a &lt;a href= "https://www.microbe.tv/contribute"&gt;patron&lt;/a&gt; of Matters Microbial!&lt;/p&gt; &lt;h3 id="links-for-this-episode" class="wp-block-heading"&gt;Links for this episode&lt;/h3&gt; &lt;ul class="wp-block-list"&gt; &lt;li&gt;&lt;a href= "https://pmc.ncbi.nlm.nih.gov/articles/PMC10025686/"&gt;Microbial "Dark Matter&lt;/a&gt;"—unknown genes in microbial genomes.&lt;/li&gt; &lt;li&gt;The process of &lt;a href= "https://www.biorxiv.org/content/10.1101/2024.04.15.589591v1.full"&gt;annotation&lt;/a&gt;.&lt;/li&gt; &lt;li&gt;An &lt;a href= "https://pubmed.ncbi.nlm.nih.gov/37610616/"&gt;article&lt;/a&gt; about the "Y-ome" or understanding "uncharacterized" genes.&lt;/li&gt; &lt;li&gt;The smallest independently growing (and engineered) bacterium, &lt;a href= "https://www.jcvi.org/research/first-minimal-synthetic-bacterial-cell"&gt;JCVI-&lt;em&gt;syn&lt;/em&gt;3.0&lt;/a&gt;. It still has many "uncharacterized" but necessary genes.&lt;/li&gt; &lt;li&gt;An &lt;a href= "https://microbewiki.kenyon.edu/index.php/Enterococcus_faecalis"&gt;essay&lt;/a&gt; on &lt;em&gt;Enterococcus faecalis&lt;/em&gt;. &lt;/li&gt; &lt;li&gt;&lt;a href= "https://wwwnc.cdc.gov/eid/article/4/2/98-0211_article"&gt;Diseases&lt;/a&gt; caused by &lt;em&gt;Enterococcus&lt;/em&gt;.&lt;/li&gt; &lt;li&gt;The concept of the &lt;a href= "https://www.cell.com/trends/microbiology/fulltext/S0966-842X(20)30104-9#:~:text=Article%20metrics-,Highlights,they%20may%20in%20fact%20have."&gt;pathobiont&lt;/a&gt;.&lt;/li&gt; &lt;li&gt;Dr. Arturo Casadevall's t&lt;a href= "https://asm.org/articles/2024/june/pathogenesis-not-a-trait-its-an-outcome"&gt;houghts on the term "pathogen&lt;/a&gt;."&lt;/li&gt; &lt;li&gt;The use of &lt;a href= "https://youtu.be/QuQoOk1M2tE?si=6xLBR6rdKM2DymoZ"&gt;transposon mutagenesis&lt;/a&gt; to create "knock outs" of bacterial genes.&lt;/li&gt; &lt;li&gt;Array &lt;a href= "https://youtu.be/BR63q_dj21M?si=KYWjOk8yIfF_htPN"&gt;transposon mutagenesis&lt;/a&gt;. Here is an &lt;a href= "https://pubmed.ncbi.nlm.nih.gov/37432110/"&gt;article&lt;/a&gt; coauthored by Dr. Willett on that topic.&lt;/li&gt; &lt;li&gt;The &lt;a href="https://alphafold.ebi.ac.uk/"&gt;Alpha Fold program&lt;/a&gt; for predicting gene function.&lt;/li&gt; &lt;li&gt;A &lt;a href= "https://youtu.be/M6VgmwqfoNU?si=a8obNgU6neBFjUYx"&gt;webinar&lt;/a&gt; describing "Microbial Dark Matter" by Dr. Willett.&lt;/li&gt; &lt;li&gt;Dr. Willett's &lt;a href= "https://med.umn.edu/bio/julia-willett"&gt;faculty website&lt;/a&gt;.&lt;/li&gt; &lt;li&gt;Dr. Willett's &lt;a href= "https://www.willettmicrolab.com/home"&gt;laboratory website&lt;/a&gt;.&lt;/li&gt; &lt;/ul&gt; &lt;p&gt;Intro music is by Reber Clark&lt;/p&gt; &lt;p&gt;Send your questions and comments to mattersmicrobial@gmail.com&lt;/p&gt; &lt;/div&gt;</description>

Matters Microbial

Mark O. Martin

Matters Microbial #119: Investigating Microbial "Dark Matter"

DEC 22, 202561 MIN
Matters Microbial

Matters Microbial #119: Investigating Microbial "Dark Matter"

DEC 22, 202561 MIN

Description

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 Subscribe: Apple Podcasts, Spotify Become a patron of Matters Microbial! 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 [email protected]