Matters Microbial

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]

Matters Microbial #118: Biofilms Everywhere! December 15, 2025 Today Dr. Matthew Fields, Director of the Center for Biofilm Engineering at Montana State University, joins the #QualityQuorum to discuss ubiquitous microbial biofilms. These biofilms touch so many aspects of life on Earth, ranging from human health to engineering issues! Host: Mark O. Martin Guest: Matthew Fields Subscribe: Apple Podcasts, Spotify Become a patron of Matters Microbial! Links for this episode The website for the American Society for Microbiology's Conference for Undergraduate Educators. Highly recommended! The must-read story of Angelina Hesse, and the first use of agar to solidify microbiological media. Here is a Kickstarter project involving promoting this important piece of microbiological history. And here is a video made by former podcast guest Dave Westenberg on the Hesse agar story. An engaging video for budding #Micronauts explaining the general concept of quorum sensing in bacteria. A video overview of biofilms on Earth. Perhaps we should call Earth "Planet Biofilm"! Here is an older review of biofilms that is very easy to read and fun to think about. Here is a newer review of the impact that biofilms can have in health, agriculture, industry, and ecology. A video interview with the late "father" of biofilm research, William J. Costerton. The concept that stromatolites are fossilized biofilms. A video describing the biofilm "life cycle." Recent developments in the details of how biofilms form. An article on biofilms and evolution of multicellularity. Previous podcast guest Dr. Vaughn Cooper's "Evolving STEM" outreach project that places biofilms front and center. The challenge of antibiotic resistance and biofilms. The website of the Center for Biofilm Engineering at Montana State University. There is so much to see here, at every level. It is a grand resource for anyone interested in biofilms. The Center for Biofilm Engineers "fact page" on biofilms. Dr. Fields' research page, where you can find information about the kinds of projects discussed today. An engaging video from Dr. Fields institution on biofilms. Dr. Fields' faculty page. Intro music is by Reber Clark Send your questions and comments to [email protected]

Matters Microbial #117: Cancer Virus Hunters and Molecular Biology December 8, 2025 Today Dr. Gregory Morgan, Professor in the School of Humanities, Arts, and Social Sciences at Stevens Institute of Technology, joins the #QualityQuorum to discuss how cancer causing viruses advanced molecular biology as described in his recent book Cancer Virus Hunters. Host: Mark O. Martin Guest: Gregory Morgan Subscribe: Apple Podcasts, Spotify Become a patron of Matters Microbial! Links for this episode Here is a link to Dr. Morgan's book on the topic discussed today. A lovely interview with Dr. Morgan about his book. A great history of molecular biology, "Eighth Day of Creation" by Horace Freeland Judson. The History and Philosophy of Science program at the University of Pittsburgh. An overview of the Rous Sarcoma Virus. A biography of Dr. Peyton Rous. A video describing how RSV causes cancer by "stealing" normal genes. How some viruses may contribute to the development of cancer. Here is another video on that topic. The field of tumor virology. A really wonderful video on the genetic origin for cancer. An overview of oncogenes and protooncogenes. A video exploring how proto-oncogenes become oncogenes, and can contribute to the development of cancer. The concept of "contagious cancer" that is rare but exists. The story of papilloma viruses and "jackalopes." The history of Cold Spring Harbor Laboratory. An overview of retroviruses. Retroviruses and FeLV. Blue chicken eggs and ancient retroviruses. A summary for novice #Micronauts. Mammalian (including human) placenta and ancient retroviruses. Nixon's "War on Cancer." An overview of the src gene. An overview of the ras gene. An overview of the p53 gene. A video explainer of the enzyme reverse transcriptase. A biography of Howard Temin. A biography of David Baltimore. The story of Human Papillovirus (HPV) and cancer. Dr. Morgan's faculty website. Intro music is by Reber Clark Send your questions and comments to [email protected]

Matters Microbial #116: Microbes in the Concrete Instead of the Abstract November 14, 2025 Today Dr. Julie Maresca, Associate Professor in the Department of Chemistry at the SUNY College of Environmental Science and Forestry joins the #QualityQuorum to discuss how bacteria can interact with a ubiquitous part of modern life: concrete! Host: Mark O. Martin Guest: Julie Maresca Subscribe: Apple Podcasts, Spotify Become a patron of Matters Microbial! Links for this episode Hartiful, the vendor that makes the enamel pins I often show on the podcast. An overview of microbes and the "built environment." An article about how concrete is made. A video on how concrete is made. The concept of "self repairing" concrete. An overview of the microbial limits to life with regard to pH. A description of alkalinophilic bacteria. Biofilms that form on concrete. Difficulties in obtaining DNA from rock. An overview of oligotrophic microbes. The alkali-silica reaction in concrete. Challenges of road salt and concrete. An overview of halophilic microbes. An overview of xerophilic microbes. The concept of SLiME communities. The term aeonophiles. Is "Roman" concrete self-repairing? A company that produces "microbial concrete." An article relevant to today's discussion by Dr. Maresca and colleagues. Dr. Maresca's faculty website. Dr. Maresca's wonderful and artistic research website. Intro music is by Reber Clark Send your questions and comments to [email protected]

Matters Microbial #115: Suiting Up Against Bacterial Predators! November 6, 2025 Today Dr. Hannah Ledvina, Assistant Professor in the Molecular, Cellular, and Developmental Biology Department at the University of Michigan joins the #QualityQuorum to discuss how bacteria can protect themselves against predators in unusual ways . . . including a type of armor! Host: Mark O. Martin Guest: Hannah Ledvina Subscribe: Apple Podcasts, Spotify Become a patron of Matters Microbial! Links for this episode The "Giant Microbes" website. A prompt for my course: an article on "Animals in a Microbial World," with so many interesting examples. Here is a summary for novice #Micronauts. A prompt for my course: an article by the late, great Lynn Margulis on the nature of kefir grains and the definition of multicellularity and the organism. A prompt for my course: an article on hyperpolyploidy in bacteria. An explanation of "genomic islands." A link to a previous guest of #MattersMicrobial, Dr. Laura Williams, discussing Bdellovibrio and undergraduate based research. An overview of predatory bacteria. Here is a more recent overview. An overview of the predator Myxococcus. A wonderful video showing the predatory process of Myxococcus. A fine review of the predator Bdellovibrio. A video of the life cycle of Bdellovibrio. Some work by Dr. Koval and colleagues suggesting that aspects of the outer cell wall is not involved with resistance to Bdellovibrio. Recent VERY exciting work suggesting that there is indeed a receptor on bacteria that Bdellovibrio can recognize. Here is a short summary of that work. Could Bdellovibrio become a "living antibiotic"? A reminder from Drs. Kolter and Losick that bacteria in the laboratory can be quite different from their relatives in nature. The article under discussion on this podcast by Dr. Ledvina and colleagues. Here is an editorial summary on the article. An article on curli proteins in bacteria. An article on amyloid like proteins in bacteria. A video by Dr. Ledvina on the research interests of her group. Thoughts on an "immune system" for bacteria. Dr. Ledvina's faculty website. Dr. Ledvina's research group website. Intro music is by Reber Clark Send your questions and comments to [email protected]