Matters Microbial #126: Squid Eggs Come With Antifungal Frosting March 24, 2026

Today Dr. Spencer Nyholm, Professor in the Department of Molecular and Cell Biology at the University of Connecticut, and Director of the Professional Science Master's Program in Microbial Systems Analysis, joins the Quality Quorum to discuss his research group's work exploring how some squid have harnessed microbes to protect their eggs against pathogens!

Host: Mark O. Martin

Guest: Spencer Nyholm

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Links for this episode

• Here is an overview of coral reef symbioses.
• The website for the famed Microbial Diversity course at the Marine Biological Laboratory at Woods Hole—a superb and life changing experience for any microbial scientist.
• An extremely fun video by Ed Yong (featuring Dr. Ned Ruby and Dr. Margaret McFall-Ngai) about the Euprymna scolopes – Vibrio fischeri symbiosis.
• Prior #MattersMicrobial podcasts related to Euprymna scolopes symbioses from Dr. Ruth Isenberg, Dr. Mark Mandel, and Dr. Margaret McFall-Ngai.
• The website for Dr. Ruby and Dr. McFall-Ngai which is so very worth your time.
• An overview of the power of confocal laser microscopy.
• The Clasi-FISH technique developed by Dr. Jessica Mark Welch (who also was on this podcast, here).
• The mass spectrometry approach to learning about small bioactive molecules, used by Dr. Marcy Balunas (who also was on this podcast, here).
• The concept of lightsheet microscopy.
• Dr. Nyholm discussed his article during the podcast, an overall review of the squid-Vibrio symbiosis.
• Dr. Nyholm discussed this article during the podcast, from his research team, describing how accessory nidemental gland microbes can protect squid eggs from fungal attack.
• Dr. Nyholm discussed this article during the podcast, from his research team, describing the development of the accessory nidemental gland and its microbiota.
• Dr. Nyholm discussed this article during the podcast, describing early work from his research team (including a former undergraduate student of mine!), exploring the microbes associated with the ANG.
• Concerns about fungal disease and global climate change, described by Dr. Arturo Casadevall (who was on this podcast, here).
• Searching for BGCs (biosynthetic gene clusters) in hopes of finding antimicrobial compounds.
• A link to Dr. Nyholm's faculty webpage.
• A link to Dr. Nyholm's laboratory group webpage.

Intro music is by Reber Clark

Send your questions and comments to [email protected]

Matters Microbial #125: Antibiotics, Streptomyces and Evolution March 15, 2026

Today Professor Paul Hoskisson, Royal Academy of Engineering Research Chair in Engineering Biology at the University of Strathclyde joins the Quality Quorum to discuss his research group's adventures studying how the bacterium Streptomyces develops, produces antibiotics, and evolves!

Host: Mark O. Martin

Guest: Paul Hoskisson

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Links for this episode

• Here is a biographical sketch of the impact of Carl Woese on microbiology.
• Here is a fine (if dated) video describing Woese's impact and work. It's truly wonderful to hear Woese himself discuss his work and challenges.
• Yours truly wrote an essay on Carl Woese and undergraduate education.
• An article on geosmin and actinobacteria. It may smell like soil, but it has other functions, like attracting springtails!
• An overview of the genus Streptomyces.
• A video showing the beauty of the life cycle of Streptomyces and various interactions.
• Linear genomes in bacteria.
• An overview of antibiotics.
• Selman Waksman and early antibiotics. And a Nobel Prize!
• The remarkable Julian Davies and antibiotic function.
• Davies' concept of small molecules with functions: the parvome.
• A wonderful collection of articles in honor of Julian Davies.
• The antibiotic resistance crisis that we all face.
• Rapamycin and the organism that synthesizes that compound, which is an immunosuppressant helpful in organ transplantation.
• The concept of Biosynthetic Gene Clusters (BGC).
• Rich Lenski and the LTEE program to study evolution in bacteria.
• A wonderful video of Dr. Lenski discussing that program.
• The use of "evolution in the lab" with bacteria to develop new functions and activities.
• Possibility of "evolution proof" antibiotics.
• Work discussed during this podcast from Dr. Hoskisson's laboratory group exploring experimental evolution in Streptomyces.
• Work discussed during this podcast from Dr. Hoskisson's laboratory group investigating the evolution of natural product synthesis.
• Work discussed during this podcast from Dr. Hoskisson's laboratory group investigating the known and unknown genes involved with secondary metabolite production.
• Dr. Hoskisson's laboratory group website.
• Dr. Hoskisson's faculty website.

Intro music is by Reber Clark

Send your questions and comments to [email protected]

Matters Microbial #124: How Bacteria Die in the Microbial Marine Forest February 24, 2026

Today Dr. Anne Thompson, Research Assistant Professor in the Department of Biology at Portland State University, joins the #QualityQuorum to discuss the small but necessary microbes in our oceans. They are hugely abundant, use strategies that produce the very oxygen we breathe, and live within an unseen marine jungle!

Host: Mark O. Martin

Guest: Anne Thompson

Download MM124 (37 MB MP3, 62 mins)

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Links for this episode

• Here is a wonderful essay about the marine cyanobacterium Prochlorococcus, probably the most abundant photosynthetic organism on Earth.
• Here is a wonderful presentation about the marine bacterium Pelagibacter, likely the most abundant organism on the planet.
• Here is a wonderful TED talk by the inspirational Dr. Penny Chisolm of MIT about the wonders of Prochlorococcus. PLEASE watch this wonderful video by a wonderful and inspiring scientist.
• A description of the Great Oxidation Event, caused by early cyanobacteria, which changed our planet.
• A lovely and fascinating essay about microbial numbers in the ocean and other ecosystems.
• A video overview of flow cytometry, which was essential to understanding the very small microbes in the ocean.
• A Scientific American article about the "Invisible Forest" of marine microbes, by Falkowski.
• A video overview of the picocyanobacteria, including Synechococcus and previously discussed Prochlorococcus.
• The essential work of Dr. John Waterbury of the Woods Hole Oceanographic Institute and photosynthetic marine microbes.
• An overview of the predators of the marine picocyanobacteria by Dr. Thompson and collaborators.
• The work of Dr. Kelly Sutherland of the University of Oregon, who collaborates with Dr. Thompson.
• A video describing the wonderfully strange choanoflagellates, which may resemble the first multicellular organisms on our planet, discussed on the podcast.
• The "mucus nets" of the organisms that Dr. Thompson and collaborators study, which may prey upon picocyanobacteria.
• A very clear overview of the research interests of Dr. Thompson and her coworkers.
• A nice video by Dr. Thompson about her research.
• Dr. Thompson's faculty website at Portland State University.
• Dr. Thompson's wonderful laboratory website.
• The website for an upcoming book that Dr. Thompson is preparing on the microbial marine forest and its importance to life on Earth.

Intro music is by Reber Clark

Send your questions and comments to [email protected]

Matters Microbial #123: What Whooping Cough Can Teach Us February 6, 2026

Today Dr. Seema Mattoo, Associate Professor of Biological Sciences at Purdue University, joins the #QualityQuorum to discuss the fascinating molecular genetics of the bacterium Bordetella pertussis, which can cause the human disease whooping cough.

Host: Mark O. Martin

Guest: Seema Mattoo

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Links for this episode

• Here is a link to Tiffany Ard's fine science related art.
• CDC information regarding Whooping Cough also called pertussis.
• An overview of the causative agent of whooping cough, Bordetella pertussis.
• A video about pertussis and its symptoms and treatment.
• More detail about B. pertussis and close relatives.
• Recent outbreaks of pertussis.
• An overview of vaccine development and its history for B. pertussis.
• An article about vaccine hesitancy and the return of childhood diseases like pertussis.
• Information on "whole cell" versus "acellular" vaccines.
• An article discussed today, demonstrating that the same molecule (a fragment of bacterial cell wall peptidoglycan) can be a factor for disease in humans, and facilitate symbiotic light organ development in the Hawai'ian Bobtail Squid
• More information of B. pertussis' trachael cytotoxin, or TCT.
• An overview of bacterial effectors interacting with our physiology in general.
• The concept of virulence factors.
• IgA versus IgG responses to infections.
• An overview of Type III Secretion Systems.
• An overview of sigma factors in bacteria.
• ECFs as sigma factors.
• Partner-switching studies.
• Fic genes.
• An overview of post translational modification.
• An essay on Theodosius Dobzhansky and his famous maxim.
• Protein misfolding and disease.
• The role of mentorship in science.
• The Hypothesis Fund and its aims.
• An article by Dr. Mattoo and colleagues discussed today about partner switching and Type III Secretion Systems.
• An article by Dr. Mattoo and colleagues discussed today about Fic proteins and adenylation.
• An article by Dr. Mattoo and colleagues discussed today about Fic proteins, post translational modification, and Parkinson's Disease.
• An article by Dr. Mattoo and colleagues discussed today about AMPylation, Fic proteins, and sensing misfolding in the endoplasmic reticulum.
• Dr. Mattoo's faculty website.
• The fascinating laboratory website of Dr. Mattoo and colleagues.

Intro music is by Reber Clark

Send your questions and comments to [email protected]

Matters Microbial #122: Jumbo Marine Viruses and Nanoscopic Warfare January 26, 2026

Today Dr. Alaina Weinheimer, Simons Foundation Postdoctoral Fellow in Marine Microbial Ecology at the Bigelow Laboratory for Ocean Sciences, joins the #QualityQuorum to discuss new and intriguing marine viruses, including Jumbo Phages!

Host: Mark O. Martin

Guest: Alaina Weinheimer

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Links for this episode

• A video overview of the wonderful world of bacterial viruses, or bacteriophages.
• A review article describing the roles that bacterial viruses can play in ecology.
• A description of changes in viral taxonomy, leading to the "realms" concept.
• An overview of "jumbo phages."
• Dr. Weinheimer's concept of "wumbology" from the cartoon "Spongebob Squarepants."
• An article describing host defenses found within bacteriophage genomes.
• An article by Dr. Weinheimer and colleagues describing lysogeny as a "plastic trait," and the possibility that all bacterial viruses can integrate into host genomes.
• The Bigelow Laboratory for Ocean Sciences website.
• The Bigelow Laboratory multimedia site.
• The webpage for the "Single Cell Genomics Center" at the Bigelow Laboratory.
• An article by Dr. Weinheimer and colleagues on exploring marine "jumbo phages."
• Marine "jumbo phages" blogpost for novice micronauts.
• An article about finding uridine within viral DNA genomes.
• Dr. Weinheimer's five minute talk about her research—highly recommended.
• The "Oceans on Tap" Facebook page describing marine biological research at the Bigelow Laboratory..
• The Simons Foundation website (which has sadly eliminated the postdoctoral fellowship awarded to Dr. Weinheimer for her work).
• Dr. Weinheimer's personal website, including background and research interests.

Intro music is by Reber Clark

Send your questions and comments to [email protected]

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

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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

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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

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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 [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

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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 [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

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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 [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

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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 [email protected]