Matters Microbial

Matters Microbial #121: Phollowing Phage in the Gut Microbiome January 7, 2026 Today Dr. Liz de Ora Ortiz, postdoctoral scholar in the Secor Laboratory at Montana State University, joins the #QualityQuorum to discuss a fascinating new technology that allows investigators to follow bacteriophage infections in live animals.   Host: Mark O. Martin Guest: Liz de Ora Ortiz Subscribe: Apple Podcasts, Spotify Become a patron of Matters Microbial! Links for this episode The fascinating and frustrating (for researchers like me) story of Vampirococcus. A Vampirococcus summary for new #Micronauts. An overview of Agrobacterium, a bacterium about which all micronauts should know (think about genetic engineering in agriculture!). The story of Pelagibacter, very probably the most abundant organism on Earth.    The story of Akkermansia, and its impact on metabolic health and the gut microbiome. An important essay by the late Dr. Elio Schaechter regarding paradigm shifts in microbiology.  Much recommended! A truly wonderful video about bacteriophages and their importance. A simple video explaining the life cycle of lytic and lysogenic bacteriophages. A video from the American Society of Microbiology linking CRISPR and bacteriophages. A review of genes "hitchhiking" in bacteriophages. An introduction to Phollow technology. An overview and discussion of the Phollow technology discussed in this podcast (paywalled).   A Phollow related publication also discussed during the podcast. The Wiles laboratory, where Dr. de Ora Ortiz and colleagues developed the Phollow technology. Dr. Travis Wiles' episode of #MattersMicrobial.  The Secor laboratory, where Dr. de Ora Ortiz currently works. Dr. de Ora Ortiz's LinkedIn profile. Intro music is by Reber Clark Send your questions and comments to [email protected]

Matters Microbial #120: Bacterial Interactions among Oral Microbes December 29, 2025 For Episode 120, we welcome Dr. Batbileg Bor, Associate Professor at the ADA Forsyth Institute, to the #QualityQuorum. He joins us to discuss some of the oral community's most enigmatic members: microbes that dwell on other microbes and potentially influence our own health. Host: Mark O. Martin Guest: Batbileg Bor Subscribe: Apple Podcasts, Spotify Become a patron of Matters Microbial! Links for this episode Here is a fun video about #LuxArt that Dr. Jennifer Quinn and I made for Harvard University's Microbial Sciences Initiative in 2024. Here is a wonderful essay about Dr. Rita Colwell.  Here is a link to her fascinating book about her life. A blog overview of the amazing Deinococcus radiodurans. A fine article about the "artwork" that Paenibacillus creates when it forms colonies. Here is the video that two of my #Bio350 #Micronauts made…a parody of Vanilla Ice's "Ice, Ice, Baby" but about microbiology. Here is a link to the #MattersMicrobial podcast involving the fascinating work of Dr. Jessica Mark Welch on the oral microbiome. A review article on predatory bacteria. An overview of the CPR (Candidate Phyla Radiation), both prominent and mysterious. A recent article by Dr. Bor and colleagues describing the "microbial dark matter" seemingly everwhere…even in the human mouth. An introductory profile on TM7, Saccharibacteria. A solid early review of TM7, by Dr. Bor and colleagues. Dr. Bor and colleagues' early article about TM7, discussed in today's podcast.   Dr. Bor and colleagues' article describing interesting interactions between the epibiont and the basibiont, described in today's podcast.  Here is a related article. An article by Dr. Bor and colleagues describing the two Type IV pili systems of Saccharibacteria. A fascinating article by Dr. Bor and colleagues describing how TM7 can modulate the responses of animals in different ways, discussed on the podcast. Dr. Bor's LinkedIn profile. Dr. Bor's faculty page at the ADA Forsyth Institute. Dr. Bor's laboratory website with fabulous images to enjoy. Intro music is by Reber Clark Send your questions and comments to [email protected]

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]