Matters Microbial

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
Subscribe: Apple Podcasts, Spotify
Become a patron of Matters Microbial!
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
Subscribe: Apple Podcasts, Spotify
Become a patron of Matters Microbial!
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
Subscribe: Apple Podcasts, Spotify
Become a patron of Matters Microbial!
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
Subscribe: Apple Podcasts, Spotify
Become a patron of Matters Microbial!
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)
Subscribe: Apple Podcasts, Spotify
Become a patron of Matters Microbial!
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]