Matters Microbial

Latest Episodes:

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

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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

Matters Microbial #118: Biofilms Everywhere! Dec 16, 2025

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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

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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 mattersmicrobial@gmail.com

Matters Microbial #117: Cancer Virus Hunters and Molecular Biology Dec 08, 2025

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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

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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 mattersmicrobial@gmail.com

Matters Microbial #116: Microbes in the Concrete Instead of the Abstract Nov 14, 2025

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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

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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 mattersmicrobial@gmail.com

Matters Microbial #115: Suiting Up Against Bacterial Predators! Nov 07, 2025

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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

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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 mattersmicrobial@gmail.com

Matters Microbial #114: A Tongue-n-Cheek Look at the Oral Microbiome Oct 31, 2025

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Matters Microbial #114: A Tongue-n-Cheek Look at the Oral Microbiome October 31, 2025

Today Dr. Jessica Mark Welch, Professor at the ADA Forsyth Institute joins the #QualityQuorum to discuss the complex and interactive microbial communities living unseen within our mouths . . . and what those communities can tell us.

Host: Mark O. Martin

Guest: Jessica Mark Welch

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Links for this episode

Here is a link to the very funny Carisa Hendrix's character "Lucy Darling." I think I made a #Micronaut out of her!
A link to the wonderful microbiological art of Dr. Lizah van der Aart.
An overview of FISH technology for visualizing DNA and microbes.
A reference to R2A medium which helps grow water associated microbes.
The anatomy of the human tongue.
The infamous and very interesting article describing how microbes are transmitted between partners via kissing.
An overview of the oral microbiome.
The relationship between oral microbiota and blood pressure.
An article by Dr. Mark Welch and colleagues describing a method for visualizing oral microbial communities.
An article by Dr. Mark Welch and colleagues about how her techniques can study the kelp microbiome microbiogeography.
An article by Dr. Mark Welch and colleagues about the oral microbiome.
An article by Dr. Mark Welch and colleagues about the unusual "corncob" microbes to be found on the human tongue.
An article by Dr. Jo Handelsman and colleagues describing the THOR soil community, in which even a few members create very diverse responses to the environment.
An article by Dr. Mark Welch and colleagues about the role of mucus in the oral microbiome.
An overview of the Forsyth Institute and its mission.
The Human Oral Microbiome Database website.
The website for Dr. Mark Welch.
A fun video snippet with Dr. Mark Welch.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #113: Microbes That Swim, Swarm, Stand Up—and 'Walk' Oct 24, 2025

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Matters Microbial #113: Microbes That Swim, Swarm, Stand Up—and 'Walk' October 24, 2025

Today Dr. Joshua Shrout, Professor of Civil and Environmental Engineering and Earth Sciences at the University of Notre Dame joins the #QualityQuorum to discuss the work of his research team on sociomicrobiology. This includes how bacteria sense a surface, move together in groups, and communicate with one another.

Host: Mark O. Martin

Guest: Joshua Shrout

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Links for this episode

Here is a wonderful video about the late great Dr. Esther Lederberg. Here is another article on that same subject.
Here is an article about prodigiosin synthesis and Serratia marcescens.
An introduction to the concept of sociomicrobiology.
An overview of bacterial swarming. Here is a wonderful swarming video.
An overview of bacterial swimming in liquid.
An article about group/social motility in Myxococcus.
A fine video explaining the amazing bacterial flagellar motor.
An article about Vibrio parahaemolyticus and swarming.
An overview of quorum sensing.
Bacteria cultivated in the laboratory undergo mutational changes during "domestication."
Pigments produced by Pseudomonas, including pyoverdin and pyocyanin.
An article from Dr. Shrout's laboratory group describing interactions between Pseudomonas and Enterococcus described in this episode.
The Type IV pili-based motility system.
An article from Dr. Shrout's laboratory describing how Pseudomonas can "walk" on one pole during swarming.
Here is a video from Dr. Shrout's laboratory showing Pseudomonas "walking" on their poles.
An overview video of the Shrout laboratory's research interests.
Dr. Shrout's faculty website.
Dr. Shrout's truly beautiful research website. There are wonderful microbial videos there. Very much worth your time.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #112: Bacterial Size, Stress, and Antibiotic Resistance Oct 17, 2025

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Matters Microbial #112: Bacterial Size, Stress, and Antibiotic Resistance October 17, 2025

Today Dr. Petra Levin, the George and Irene Freiberg Professor of Biology at Washington University in St. Louis joins the #QualityQuorum to discuss her work with bacterial cell size, environmental stress on bacteria, and antibiotic resistance.

Host: Mark O. Martin

Guest: Petra Levin

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Links for this episode

An overview of the periplasm, found in Gram negative bacteria.
An overview of beta-lactam antibiotics.
The field of quantitative microbiology.
An overview of B. subtilis.
An overview of E. coli.
An overview of Klebsiella.
The biography of Barbara McClintock, "A Feeling for the Organism."
A video explanation of the lac operon of E. coli.
The LTEE program (Long Term Evolution Experiment) founded by Dr. Rich Lenski.
The nomenclature of monoderm and diderm bacteria.
A video explanation of peptidoglycan in bacteria.
Penicillin binding proteins (PBP) and antibiotic resistance.
A video about cell division in E. coli.
A famous article coauthored by Dr. Elio Schaechter that describes cell growth and cell size in bacteria.
A related article by Dr. Levin and colleagues.
An overview of ESKAPE bacteria.
An article from Dr. Levin's research group describing the relationship between pH and antibiotic resistance.
An article about persister cells and their relevance to antibiotic resistance.
Dr. Levin's faculty website.
Dr. Levin's very interesting laboratory website.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #111: Shocking Tales of Metal-Loving Microbes Oct 10, 2025

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Matters Microbial #111: Shocking Tales of Metal-Loving Microbes October 10, 2025

Today Dr. Jeff Gralnick, Professor of the Department of Plant and Microbial Sciences at the University of Minnesota joins the #QualityQuorum to tell us a shocking story about how his research group studies the relationship between electrons, microbes, and metals.

Host: Mark O. Martin

Guest: Jeff Gralnick

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Links for this episode

An article about Nobel Prize winner Albert Szent-Györgyi.
The Soudan Formation Iron Mine discussed during the podcast.
An article on Banded Iron Formations.
An article about the Oxygen Crisis early in Earth's history.
An overview of the bacterium Shewanella.
An overview of the bacterium Geobacter.
An overview of microbial redox reactions.
The "bacterial battery" we discussed: the Mudwatt.
An article on benthic microbial fuel cells.
An article on extracellular electron transfer by bacteria.
The laboratory of Dr. Daniel Bond at the University of Minnesota, and colleague of Dr. Gralnick's.
An essay on microbial nanowires.
An essay on cable bacteria, which was the topic of #MattersMicrobial podcast #101 with Dr. Nicole Geerlings.
The new field of electromicrobiology.
The relationship between Shewanella and fish! An article by Dr. Gralnick and colleagues on the Shewanella and fish (and bacteriophage) association.
The article about Jon Beckwith (by Howard Shuman) discussed in the podcast: "With Toothpicks and Logic."
Dr. Gralnick's faculty website.
Dr. Gralnick's laboratory website.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #110: Enumerating the Microbiome Oct 03, 2025

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Matters Microbial #110: Enumerating the Microbiome October 3, 2025

Today Dr. Sean Gibbons, Associate Professor at the Institute for Systems Biology, returns to the #QualityQuorum to tell us about how he and his colleagues are able to listen very carefully to the microbiome to uncover important hints about health.

Host: Mark O. Martin

Guest: Sean Gibbons

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Links for this episode

Here is the article from Dr. Norm Pace and coworkers on the showerhead microbiome referenced in the podcast.
Here is a nonspecialist summary of Dr. Pace's work on the showerhead microbiome and mycobacteria.
Here is a link to a prior episode of this podcast with Dr. Ameet Pinto on microbiology of the water supply.
Here is Dr. Gibbon's earlier visit to this podcast.
An overview of the difference between microbiome and microbiota.
An article about the "misnumbering" of the number of microbial to human cells in people. Here is a nonspecialist summary.
An overview of metagenomics.
An overview of qPCR.
An overview of flow cytometry.
Plato's Allegory of the Cave, discussed in this podcast.
A cautionary tale about determining a cancer microbiome, as discussed in this podcast.
An article by Dr. Gibbons and colleagues described in this podcast about how to estimate microbial biomass directly.
An article by Dr. Gibbons and colleagues described in this podcast about how to estimate microbial growth rates in the human gut using metagenomics.
An article by Dr. Gibbons and colleagues described in this podcast about how to use metagenomics to determine dietary habits.
The website for Dr. Gibbon's research group.
The faculty website for Dr. Gibbons at ISB.
Courses on microbiome sciences online at ISB.
The website for Institute for Systems Biology.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

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