Matters Microbial

Matters Microbial #131: What Cystic Fibrosis Reveals About Hidden Microbial Lives
June 3, 2026 Today Dr. Sam Brown, Professor of Biological Sciences at Georgia Tech University, joins the quality quorum today to discuss the social lives of bacterial pathogens. He will also discuss VERY recent research from his lab group exploring the specialist/generalist problem in Pseudomonas aeruginosa, and thoughts on cryptic convergent specialization!
Host: Mark O. Martin
Guest: Sam Brown
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Links for this episode
An overview of behavioral ecology.
An article describing evolutionary trade offs and game theory.
A video describing Tinbergen's "Four Whys" involving behavioral ecology.
A wonderful essay by Carl Zimmer relating lake ecology and microbial ecology in humans. 
A Pseudomonas plush toy from Giant Microbes.
The Pseudomonas contaminated eyedrops story told by Dr. Brown, as summarized by the CDC.
An essay about sociomicrobiology.
An overview of quorum sensing.
An overview of biofilms.
An article describing specialization versus generalism in ecology. 
A description of a "confusion matrix" in data analysis.
A somewhat dated overview of PCA (principle component analysis).
The article about convergent cryptic specialization under discussion today on this podcast from Dr. Brown's research group (first author Mehlferber).
A VERY interesting article from Dr. Brown's research team describing eco-evolutionary aspects of polymicrobial infections.
Dr. Brown's faculty website.
Dr. Brown's laboratory group website.
Intro music is by Reber Clark
Send your questions and comments to [email protected]

Matters Microbial #130: The Holobiont — Animals, Microbes, and Ecology
May 19, 2026 Today Dr. Kevin Kohl, Associate Professor of Biological Sciences at the University of Pittsburgh, joins the #QualityQuorum to discuss how he and his colleagues study the interplay between animals, their resident gut microbes, and the overarching concept of the holobiont.
Host: Mark O. Martin
Guest: Kevin Kohl
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Links for this episode
The One Health Microbiome Center at Pennsylvania State University.
A very fine essay on the holobiont concept for non-microbiologists.
A general introductory overview of the holobiont concept.
The holobiont concept and the coral symbiosis. 
A partial history of the development of the holobiont concept.
Dr. Casadevall suggests that context and thus outcomes describes the term "pathogen," and a similar analysis applies to the holobiont.
A very short description of the holobiont concept. 
Another overview of the holobiont concept in general, coauthored by Dr. Kohl. 
Some basic rules for thinking about the holobiont concept.
A video introduction to the holobiont concept, by Dr. Seth Bordenstein.
I highly recommend this essay by the science writer Carl Zimmer, "The Human Lake," to think of the connections between lake ecology and microbial interactions with humans.
Another wonderful article recommended by Dr. Kohl, by Dr. Margaret McFall-Ngai and coauthors, detailing the impact microbes have on animals over evolution and development. 
The wood rat – creosote – microbiome connection to the holobiont concept, discussed on this podcast (coauthored by Dr. Kohl).
The fascinating work by Dr. Kohl and colleagues showing the relationship between tadpole development and pond microbes discussed in this podcast.
 A must read article by Dr. Kohl and colleagues, "Through the microbial looking glass: our shifting understanding of the holobiont and microbes as mediators of organismal biology," illustrates the development and influence of the holobiont concept.
Dr. Richard Prum's book, "Performance All the Way Down," was discussed during this podcast. There is also a video where Dr. Prum discusses the ideas in this book, describing gene regulation as a performance. 
Dr. Kohl's faculty website.
Dr. Kohl's (very interesting) research website.
Intro music is by Reber Clark
Send your questions and comments to [email protected]

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]