Matters Microbial #129: Microbes Reveal How Evolution Might Replay May 5, 2026

Today Dr. Michael Travisano, Distinguished McKnight University Professor in the College of Biological Sciences of the University of Minnesota, joins the #QualityQuorum to discuss fascinating work from his lab group exploring evolutionary questions from a microbial perspective.

Host: Mark O. Martin

Guest: Michael Travisano

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Links for this episode

• Here is the link to the article we discussed during the podcast, authored by Dr. Travisano and Dr. Rainey.
• An overview of the concept of adaptive radiation.
• The ecological/evolutionary concept of "cheating" which applies to the mat forming bacteria discussed in this podcast.
• A link to an article by Dr. Jo Handelsman and colleagues about THOR, a simple microbial community that has shows great functional diversity.
• A wonderful essay about Dr. Rich Lenski's role in the LTEE.
• An essay from "Small Things Considered" describing "rewinding" evolution using microbial systems.
• A wonderful book by Stephen Jay Gould, "Wonderful Life" about evolution.
• Another book well worth your attention: "Chance and Necessity" by Jacques Monod.
• An article about the challenges of multicellularity in bacteria.
• The wonderful short video example of "snowflake yeast" evolving within days.
• A link to another #MattersMicrobial podcast by Dr Will Ratcliff, about "snowflake yeast."
• An article by Dr. Travisano and colleagues describing conflict and cooperation in microbial societies discussed on this podcast.
• An article by Dr. Travisano and colleagues about the evolution of "snowflake yeast," discussed on this podcast.
• An article by Dr. Travisano and colleagues discussing the role of other microbes in the development of multicellularity, discussed on this podcast.
• An article by Dr. Travisano and colleagues, on the repeatability of microbial adaptive evolution discussed on this podcast.
• A list of references authored by Dr. Travisano and colleagues.
• Dr. Travisano's faculty website.

Intro music is by Reber Clark

Send your questions and comments to [email protected]

Matters Microbial #128: C. diff from Nursery to Nursing Home April 20, 2026

Today Dr. Joseph Zackular, Assistant Professor of Pathology and Laboratory Medicine at the Perelman School of Medicine at the University of Pennsylvania, joins the #QualityQuorum to discuss some fascinating microbiology involving the bacterium Clostridiodes difficile (also known as C. diff), which can cause disease in infants, the elderly, and the immunocompromised.

Host: Mark O. Martin

Guest: Joseph Zackular

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Links for this episode

• An essay about siderophores in bacteria.
• The Giant Microbes "Cdiff" toy.
• The website of Dr. Patrick Schloss.
• A link to the #MattersMicrobial podcast with Dr. Schloss.
• An overview of Clostridioides difficile from a patient / physician perspective.
• A review article of research involving Clostridioides difficile.
• An overview on polymicrobial diseases.
• A wonderful opinion piece by Dr. Arturo Casadevall regarding the term "pathogen."
• An overview of Enterococcus in the gut microbiome.
• The technology of imaging mass spectrometry.
• An article on Stickland fermentation of amino acids among gut bacteria.
• Work by Dr. Zackular and colleagues discussed in this podcast, describing how FMT can be used as a treatment.
• Work by Dr. Zackular and colleagues discussed in this podcast, describing how different members of the host microbiome interact, and how that relates to disease.
• Work by Dr. Zackular and colleagues discussed in this podcast, describing the role of amino acid metabolism to changes in microbiome structure.
• Work by Dr. Zackular and colleagues discussed in this podcast, describing how Enterococcus can modulate the disease causing characteristics of C. difficile.
• An interesting paper showing that polymicrobial effects are more common than expected.
• An article arguing that there is no single "healthy" microbiome.
• A lovely primer on this topic for most nonmicrobiologists.
• An overview on fecal microbiome transplants and the treatment of human disease.
• The website for the Center for Microbial Medicine at the University of Pennsylvania.
• A great video by Dr. Zackular and colleagues, well worth your time.
• Dr. Zackular's academic website.
• Dr. Zackular's laboratory website.

Intro music is by Reber Clark

Send your questions and comments to [email protected]

Matters Microbial #127: Even Your Navel Has Them — An Archaea‑Whisperer Explores April 7, 2026

Today Dr. Nahui Medina-Chavez, postdoctoral scholar in the Travisano laboratory at the University of Minnesota, joins the Quality Quorum to discuss her interest in the ubiquitous archaea, and her own research studying experimental evolution in extreme halophiles.

Host: Mark O. Martin

Guest: Nahui Medina-Chavez

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Links for this episode

• Here is an article on R2A, which is used to cultivate water associated microbes.
• A solid and clear article describing the "great uncultivated majority."
• An article describing the discovery of the archaea.
• An engaging video summary of the archaea.
• A recent article suggesting that archaea are the root and originator of eukaryotes like ourselves!
• An interesting video about the lokiarcheota, which contain the genetic echoes of eukaryotic life.
• An article about the extremely halophilic archaea.
• Do extreme halophiles live within salt crystals?
• The beautiful pink pigment, bacteriorhodopsin, associated with these archaea (despite the "bacterio" portion of the name).
• The LTEE experiment, describing how researchers can study evolution in the laboratory.
• Genomic islands in microbiology.
• The "Archaeal Power Hour" website.
• A fine video presentation by Dr. Medina-Chavez on archaea.
• A fine article by Dr. Medina-Chavez and her postdoctoral advisor Dr. Michael Travisano on archaeal communities.
• Dr. Medina-Chavez's Research Gate website.

Intro music is by Reber Clark

Send your questions and comments to [email protected]

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]