Matters Microbial

Matters Microbial #74: Podcasting to Combat Microbial Misinformation Jan 16, 2025

Matters Microbial #74: Podcasting to Combat Microbial Misinformation January 16, 2025

Today, Dr. Jessica Coates of the Biology Department at Spelman College joins the #QualityQuorum to discuss her work combating microbial misinformation in the classroom and to share her journey to the microbial sciences.

Host: Mark O. Martin

Guest: Jessica Coates

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Links for this episode

A short talk I gave at ASM some time ago about Louis Pasteur and the term “germ.”
An organization devoted to promoting microbial literacy.
An example of using podcasting to increase learning outcomes in the STEM classroom.
An example of using podcasts by scientists to promote learning by students.
The interesting story of Spelman College.
An interview with Dr. Coates.
The academic website of Dr. Coates.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #73: Seeing the Microbiome Jan 09, 2025

Matters Microbial #73: Seeing the Microbiome January 8, 2025

Today, Dr. Travis Wiles, Assistant Professor of Molecular Biology and Biochemistry at the University of California, Irvine, joins the #QualityQuorum to discuss the work he and his research group have done to visualize the changing dynamics of the gut microbiome—including bacteriophages residing there.

Host: Mark O. Martin

Guest: Travis Wiles

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Links for this episode

Dr Anne Estes’ academic website is found here, along with her blog, and her social media link on Bluesky. So many interesting ideas!
Transgenic zebrafish as pets are called GLOfish.
Use of zebrafish as a model system for developmental biology.
An article exploring the effects of the microbiome on gnotobiotic (“germ free”) zebrafish.
An essay on both lytic and lysogenic bacteriophages.
An essay describing how bacteriophage interact with the gut microbiota. One of my former undergraduate research students, Dr. Danielle Campbell, works in this area!
An article suggesting that bacteriophage do in fact interact with eukaryotic cells.
The concept of phage conversion: how some bacteriophages carry bacterial genes, including toxin genes.
An article about bacteriophages and bacterial evolution.
An article about the study of the zebrafish gut microbiome.
An article about research with zebrafish and Mycobacterium.
The article discussed in this episode by Dr. Wiles’ group: “Phollow: Visualizing Gut Bacteriophage Transmission within Microbial Communities and Living Animals .”
Dr. Wiles’ academic website.
Dr. Wiles’ very colorful and interesting laboratory group website.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #72: Who is in Your Water? Jan 02, 2025

Matters Microbial #72: Who is in Your Water? January 2, 2025

Today, Dr. Ameet Pinto, Carlton S. Wilder Associate Professor in Civil and Environmental Engineering at the Georgia Institute of Technology, joins the #QualityQuorum to discuss the microbiome of drinking water and how it can be used to optimize safety and health.

Host: Mark O. Martin

Guest: Ameet Pinto

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Links for this episode

A short review of a famous article by Dr. Norman Pace about the microbiome of showers and how microbial populations differed due to chlorination.
An old discussion of microbial oligotrophy: the ability to survive on very low levels of nutrients.
The story of John Snow, a water fountain, and cholera in England.
The concept of “Live/Dead” staining of microbes.
An overview of the concept of metagenomics.
An article on the microbiome of shower hoses.
A public science outreach program to study the microbiome of showerheads.
The Instagram link for Dr. Pinto’s wonderful cat, Nessie.
A great book describing exceptions to Mendelian genetics using cats: “Cats Are Not Peas.” Highly recommended.
An article about water supplies and the pathogenic microbe Legionella.
An overview of water disinfection techniques.
An introduction to a model system of a microbial soil community, called THOR by Jo Handelsman and colleagues.
Thinking of water treatment and related technologies as a series of ecological niches, via Tom Curtis and Bill Sloane.
Dr. Pinto’s faculty website.
Dr. Pinto’s deeply fascinating research group website.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #71: Disinfecting the Built Environment Dec 26, 2024

Matters Microbial #71: Disinfecting the Built Environment December 25, 2024

Ever wonder what’s growing on your toothbrush? Today, Dr. Erica Hartmann, Associate Professor of Civil and Environmental Engineering at Northwestern University, joins the #QualityQuorum to discuss how antimicrobial resistance can occur in the built environment we see all around us every day—and why it is vital to learn more about this association.

Host: Mark O. Martin

Guest: Erica Hartmann

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Links for this episode

An essay on the Hygiene Hypothesis.
An overview of the “built environment.”
The trouble with triclosan.
An essay on heavy metal resistance.
An article from Dr. Hartmann’s group about the toothbrush microbiome (“Project Pottymouth”).
A link to the Human Microbiome Project.
An overview of antibiotic resistance and antibiotic resistance genes.
An article about silver nanoparticles on toothbrushes.
A blog post about probiotic cleaning products.
An interesting post from Dr. Hartmann’s team about viruses in your bathroom.
A video by Dr. Hartmann about her research.
Dr. Hartmann’s faculty website.
Dr. Hartmann’s research team website.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #70: Food Safety and Antibiotic Resistance Dec 19, 2024

Matters Microbial #70: Food Safety and Antibiotic Resistance December 18, 2024

Today, Dr. Dr. Erika Ganda, Assistant Professor of Food Animal Microbiomes in the Department of Animal Science at Pennsylvania State University, joins the #QualityQuorum to discuss the varied interests of her research team studying the intersection of animal husbandry, microbiome studies, and the threat of antimicrobial resistance.

Host: Mark O. Martin

Guest: Erika Ganda

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Links for this episode

A video that Dr. Quinn and yours truly did for an event at Harvard University about #LuxArt.
A video of a #LuxArt event I ran at ASMCUE a few years ago.
An overview from the CDC about the One Health concept.
The story of “Typhoid Mary.”
An overview of rumen microbiology.
The glass artwork of Jane Hartman.
An article about Salmonella dublin and the impact on the dairy industry.
An introduction to strategies of antibiotic resistance.
A TED talk about the threat of antibiotic resistance.
The concept of low level antibiotics to promote growth in chickens and other animals.
A video demonstrating the swift rise of antibiotic resistance using the MEGAPLATE approach.
The accident in Brazil in 2015 releasing metal mining waste leading to increased antibiotic resistance.
Evidence that microbial zinc resistance leads to increased antibiotic resistance.
An explainer for proper antibiotic use.
Dr. Ganda’s faculty website.
Dr. Ganda’s research website

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #69: Can Eating Microbes Make You Healthy? Dec 12, 2024

Matters Microbial #69: Can Eating Microbes Make You Healthy? December 11, 2024

Today, Dr. Maria Marco, Professor of Food Science and Technology at the University of California Davis, joins the #QualityQuorum to discuss microorganisms in food, intestinal ecosystems, and the role that lactic acid bacteria can play in health and well-being.

Host: Mark O. Martin

Guest: Maria Marco

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Links for this episode

An overview of food science microbiology as a career.
An article on the microbial ecology of sauerkraut.
An article on Élie Metchnikoff and his ideas about probiotics and health/lifespan.
An overview of Lactobacillus acidophilus, and an article on its use in medical settings.
The story of E. coli Nissle.
“Wild Fermentations,” a book by Sandor Katz.
Discussion of clinical trials with probiotics.
Thoughts about indigenous microbiology.
A related essay on indigenous microbiology.
Dr. Marco’s faculty website.
Dr. Marco’s research website.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #68: Social Evolution in Viruses Dec 05, 2024

Matters Microbial #68: Social Evolution in Viruses December 4, 2024

Today, Dr. Sam Díaz-Muñoz, Assistant Professor of Microbiology and Molecular Genetics, as well as a Faculty Member of the Genome Center at the University of California Davis, joins the #QualityQuorum to discuss how their group, and a growing community of researchers, investigates the social lives of viruses: the many ways that viruses interact and the ways that interactions shape infections and viral evolution.

Host: Mark O. Martin

Guest: Sam Díaz-Muñoz

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Links for this episode

An article by Carl Zimmer on the social lives of viruses.’
An overview of RNA viruses in general.
An overview of cystoviruses.
An overview of the use of cystoviruses in the study of evolution.
A relevant article: “Open Questions in the Social Lives of Viruses,” Leeks et al. 2023:
Another relevant article: “Sociovirology: Conflict, Cooperation, and Communication among Viruses,” Díaz-Muñoz et al. 2017:
The website for the Social Lives of Viruses Meetings
An article from Jesse Bloom’s lab showing the variation in single cell infection outcomes (Figure 4 is one of Dr. Díaz-Muñoz’s favorites from any paper).
The faculty website for Dr. Lin Chao, who was very influential in Dr. Díaz-Muñoz’s background and promoted the study of evolution in microbes.
The website for Dr. Paul Turner, who was very influential in Dr. Díaz-Muñoz’s background and promoted the study of evolution in microbes.
The website for Dr. Rich Lenski, who was very influential in Dr. Díaz-Muñoz’s background and promoted the study of evolution in microbes.
A CDC article about “shift” versus “drift” in influenza.
A video by Dr. Díaz-Muñoz from 2020 about viruses.
Dr. Díaz-Muñoz’s faculty website.
Dr. Díaz-Muñoz’s laboratory group website.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #67: Chemical Communication in Microbe Symbioses Nov 28, 2024

Matters Microbial #67: Chemical Communication in Microbe Symbioses November 27, 2024

Today, Dr. Marcy Balunas, Associate Professor of Microbiology and Immunology, as well as part of the Department of Medicinal Chemistry at the University of Michigan, joins the #QualityQuorum to discuss how her group investigates the chemical signals—the language—between host and microbe symbioses.

Host: Mark O. Martin

Guest: Marcy Balunas

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Links for this episode

An article on bacterial colonial variation during domestication, by Dr. Roberto Kolter and colleagues.
The Tiny Earth Project to crowdsource new bacterial sources of antibiotic compounds.
An overview of chemical ecology.
Description of how analytical chemistry is used to investigate symbioses.
A description of how MALDI is used to identify compounds.
A description of how LC M/S is used to identify compounds.
A description of some work done on tunicate-microbe associations by the Balunas lab.
Dr. Jonathan Klassen collaboration.
An article on ant based fungal farming.
Dr. Spencer Nyholm collaboration.
An article on the squid nidamental gland.
Dr. Irene Newton collaboration.
An article on bee associated microbes that protect against fungal infection.
A video describing some of the work done by the Balunas laboratory on ant fungus farming with Dr. Klassen.
Dr. Balunas faculty website.
Balunas laboratory website.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #66: Digesting the Science of Fermented Foods Nov 21, 2024

Matters Microbial #66: Digesting the Science of Fermented Foods November 20, 2024

Today, Dr. Ben Wolfe, Associate Professor of Biology at Tufts University, joins the #QualityQuorum to discuss how he and his collaborators study novel food fermentations, helping the public understand more about the gut microbiome, and outreach projects involving microbially-associated food.

Host: Mark O. Martin

Guest: Benjamin Wolfe

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Links for this episode

An overview for beginning Micronauts on microbial fermentation.
A more advanced overview of microbial fermentation.
A book and website that I highly recommend by Sandor Katz on the subject, including many recipes and background information.
The bacterially derived volatile chemical geosmin.
An article describing the relationship between geosmin and springtails.
An article about leaf cutter ants and how they farm fungi! I hope to do an entire podcast on this topic soon.
An article of Dr. Wolfe and colleague’s work showing a relationship between fungal antibiotics and cheese microbiome development.
Dr. Rob Dunn’s “Belly Button Microbiome” project, a community science effort.
An overview of the community science effort to explore sourdough bread microbiology.
An overview of cheese microbiology.
A description of cheesemaking and cheese caves.
A cheesemaker with which Dr. Wolfe has worked.
A link to a remarkable article by Dr. Wolfe’s research group that we discussed in this episode: “Novel Fermentations Integrate Traditional Practic and Rational Design of Fermented-Food Microbiomes.”
A video of a presentation by Dr. Wolfe on cheese microbiology.
Dr. Wolfe’s faculty website at Tufts University.
A website by Dr. Wolfe and coworkers promoting microbial literacy via understanding the positive relationship between food and microbes.
The website of Dr. Wolfe’s research group.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #65: Squishy Tissues and Hints from Archaea Nov 14, 2024

Today, Dr. Alex Bisson, Assistant Professor of Biology at Brandeis University, joins the #QualityQuorum to discuss how he and his collaborators use a variety of tools to study the mechanobiology of archaea (such as how some respond to being “squished”), and how those studies can shed light on the evolution of complex eukaryotes like humans.

Host: Mark O. Martin

Guest: Alex Bisson

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Links for this episode

An overview of one of the archaea used by Dr. Bisson’s research team, Haloferax volcanii.
Here is an article from New Scientist about Dr. Bisson’s research.
A journal article from Nature Communications describing work done by the Bisson laboratory.
The preprint from Dr. Bisson’s research team discussed in this podcast.
Here is a video of a seminar by Dr. Bisson.
Dr. Bisson’s faculty website.
Dr. Bisson’s very interesting research team website.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #64: Making Sense of the Microbiome Nov 07, 2024

Today, Dr. Patrick Schloss, Professor in the Department of Microbiology and Immunology in the School of Medicine at the University of Michigan, joins the #QualityQuorum to discuss how the human microbiome is studied, possible pitfalls in such data analysis, and what tools he and his coworkers have developed to lead toward repeatable, hypothesis-driven science.

Host: Mark O. Martin

Guest: Patrick Schloss

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Links for this episode

An overview of how the gut microbiome is analyzed.
One of the articles discussed by Dr. Schloss exploring reproducibility in microbiome studies: “Identifying and Overcoming Threats to Reproducibility, Replicability, Robustness, and Generalizability in Microbiome Research.”
Another article discussed by Dr. Schloss, regarding the link between the microbiome and obesity: “Looking for a Signal in the Noise: Revisiting Obesity and the Microbiome.”
An article from Dr. Schloss’ research team that explores a link between the human microbiome and a type of colorectal cancer.
A link to the MOTHUR project, used to analyze microbiome data.
A link to a video by Dr. Schloss: “Understanding Disease Through the Lens of the Microbiome.”
Dr. Schloss’ YouTube channel about data analysis.
Dr. Schloss’ research group website.
Dr. Schloss’ faculty website.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #63: A Symphony of Cyanobacteria Oct 31, 2024

Matters Microbial #63: A Symphony of Cyanobacteria October 30, 2024

Today, Dr. Nathan Algren, Associate Professor of Biology at Clark University, joins the #QualityQuorum to discuss the centrality of cyanobacteria to our biosphere, the viruses that prey upon them, and his interests in outreach and science-oriented art.

Host: Mark O. Martin

Guest: Nathan Ahlgren

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Links for this episode

An overview of the cyanobacteria.
An overview of Prochlorococcus.
An overview of marine bacteriophages.
The Great Oxidation Event Cyanobacteria are thought to have radically changed our planet 2.5-3.5 billion years ago by producing oxygen through photosynthesis. In essence, they and other microbes are the original terraformers.
The Purple Earth Hypothesis Photosynthesis as we know it, using chlorophyll, may have evolved after another way of doing photosynthesis, with retinal that looks purple. This means that our planets and other ‘younger’ planets may look or have looked purple rather than green.
Self-assembly of viral capsids, as modeled by 3D-printed parts (Art Olson)
TED talk from Penny Chisholm on Prochlorococcus
Co-occurring Synechococcus ecotypes occupy four major oceanic regimes defined by temperature, macronutrients and iron Study showing how different populations of Synechococcus occupy different niches and regions of the oceans according to their adaptations to temperature and nutrients.
Long-term stability and Red Queen-like strain dynamics in marine viruses Study showing turnover of strains within relatively stable phage populations.
Viral treadmills in the ocean—running to stand still Companion ‘behind the paper’ article.
Diverse Marine T4-like Cyanophage Communities Are Primarily Comprised of Low-Abundance Species Including Species with Distinct Seasonal, Persistent, Occasional, or Sporadic Dynamics Paper showing cyanophage ‘species’ have different time patterns in the oceans.
Rapid diversification of coevolving marine Synechococcus and a virus Study showing stable co-existence and co-evolution of a single Synechococcus host and phage over time. The emergence of resistance hosts and phage that overcome them demonstrate the principles of the Red Queen hypothesis and phage-host ‘arms race’.
Present and future global distributions of the marine Cyanobacteria Prochlorococcus and SynechococcusFigure from this paper is in the presentation. Shows modeled distributions of Pro and Syn across the globe. They also use this to estimate a ~25% contribution of Pro and Syn to global net primary productivity in the oceans.
Link to 3D prints that Dr. Ahlgren made an are available on NIH page
Some resources on how to 3D protein structures: I like this guide on the practical guide of how to do actually to do it (going from PDB to print files):
A link to another resource for 3D printing of protein structures.
Dr. Ahlgren’s faculty website.
Dr. Ahlgren’s laboratory website with many fascinating links.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #62: Should I Stay, or Should I Go—How Bacteriophage are Released from Host Cells Oct 24, 2024

Matters Microbial #62: Should I Stay, or Should I Go—How Bacteriophage are Released from Host Cells October 23, 2024

Today, Dr. Jolene Ramsey, of the Biology Department of Texas A&M University and Affiliate of the Center for Phage Technology, joins the #QualityQuorum to discuss how bacteriophages release themselves from host cells, her efforts to teach students to work with the primary literature, and her own path to the microbial sciences.

Host: Mark O. Martin

Guest: Jolene Ramsey

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Links for this episode

A truly wonderful reminder video about bacteriophages.
A link with a 3D printer design of capsid model pieces (personally, I am really interested in making one of these!).
A video demonstrating how the capsid model pieces self assemble—something like real viruses can?
An essential book about bacteriophage authored by my late friend Merry Youle.
A fine book describing how bacteriophages can be used to fight bacterial diseases.
This “first person” book by #MattersMicrobial podcast guest Steffanie Strathdee about how she was able to use bacteriophages to save her husband’s life is a must read.
A link to the Citizen’s Phage Library.
A link to the truly fabulous (yes, I am jealous I am not part of this program) CURE program SEA-PHAGES and SEA-GENES for undergraduate students.
A remarkable illustration of T4 bacteriophage bursting from host cells by the scientist-artist David Goodsell.
The organization that designed Dr. Ramsey’s laboratory logo.
A link to the Clinical Genome Curation for Human Genes.
A link to the CACAO website for biocuration competition.
A recent Ramsey lab mini-review on phage classification.
A link to the Center for Phage Technology.
The Ramsey lab Instagram page.
The Ramsey lab YouTube channel.
Dr. Ramsey’s laboratory website.
Dr. Ramsey’s faculty website.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #61: All In Due Time–How Bacteria Wake from Dormancy Oct 17, 2024

Matters Microbial #61: All In Due Time–How Bacteria Wake from Dormancy October 17, 2024

Today, Dr. Paul Carini, of the Environmental Science department of the University of Arizona, joins the #QualityQuorum to discuss how soil bacteria can become dormant, “wake up,” and why that is more relevant than you might suppose.

Host: Mark O. Martin

Guest: Paul Carini

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Links for this episode

A lovely essay about the “Cultivation Conundrum”: why so many microbes in nature cannot be grown in the laboratory.
The “uncultivated majority” is often called “microbial dark matter,” described here.
An essay about the scale of microbiology with some fascinating facts.
Arizona Culture Collection project by Dr. Carini and colleagues.
Dilution to extinction technique
An overview of sporulation, including some fascinating variations.
A description of Arthrobacter
A description of Bradyrhizobium
An essay explaining PCA plots
An essay about intrinsically disordered proteins
A very nice video about working in Dr. Carini’s lab. HIGHLY RECOMMENDED.
Dr. Carini’s faculty website.
Dr. Carini’s fascinating laboratory website.
Dr. Carini’s Substack page, where he explores many microbiological ideas.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #60: Influenza, Epidemics, Pandemics, and Fortunate Mistakes Oct 10, 2024

Matters Microbial #60: Influenza, Epidemics, Pandemics, and Fortunate Mistakes October 9, 2024

Today, Dr. Adam Lauring of the University of Michigan joins the #QualityQuorum to discuss the job of a physician-scientist, RNA viruses, the tricks that influenza uses to create epidemics and pandemics, and the science behind flu vaccines.

Host: Mark O. Martin

Guest: Adam Lauring

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Links for this episode

A description of the MD/PhD path in science.
An introduction to RNA viruses.
An article describing different types of RNA viruses.
The history of influenza.
An overview of the influenza virus.
An essay on the shift/drift issue in influenza.
A more formal review of the shift/drift issue in influenza.
A video about the evolution of RNA viruses.
An essay about influenza virus evolution describing some of Dr. Lauring’s work.
Dr. Lauring and his colleague’s fascinating research lab page.
Dr. Lauring’s faculty website.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #59: Some (Microbes) Like It Hot—Discussions with the Thermal Biology Institute Oct 03, 2024

Matters Microbial #59: Some (Microbes) Like It Hot—Discussions with the Thermal Biology Institute October 3, 2024

Today is an unusual episode of the podcast. I am visiting four microbiologists in the Thermal Biology Institute at Montana State University of Bozeman, Montana. They discuss their work exploring the unusual microbes and environments to be found in Yellowstone National Park, ranging from the history of the park to opportunities for undergraduate students, as well as up-to-the-minute research done on the microbial denizens of this microbiological landmark.

Host: Mark O. Martin

Guests (in order of appearance:): Brent Peyton, Dana Skorupa, Zackary Jay, Anthony Kohtzy

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Links for this episode

A history and overview of Yellowstone National Park.
An overview of microbiology in Yellowstone National Park.
The story of Yellowstone National Park and PCR.
Website for the Thermal Biology Institute.
A prior podcast of #MattersMicrobial involving Dr. Roland Hatzenpichler and the research done by several of today’s guests.
Dr. Peyton’s faculty website.
Dr. Peyton’s laboratory website.
Dr. Skorupa’s faculty website.
A great article on the adventurous REU (Research Experience for Undergraduates) that Dr. Skorupa supervises.
Dr. Jay’s faculty website.
A journal article describing some of Dr. Jay’s (and Dr. Kohtz’) work.
A page including Dr. Kohtz
An article describing some of Dr. Kohtz’ (and Dr. Jay’s) work.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #58: The Virosphere from Coral Reefs to Other Worlds Sep 26, 2024

Today, Dr. Cynthia Silveira of the Department of Biology at Miami University joins the #QualityQuorum to discuss her research team’s efforts to explore how bacterial viruses interact with their host cells from coral reefs to other planets! In addition, Dr. Silveira will discuss her microbiological path and a course she teaches on virology.

Host: Mark O. Martin

Guest: Cynthia Silveira

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Links for this episode

A video about marine bacteriophages and the role they play in ecological systems.
A fine article about the role that bacteriophages can have in marine environments.
An essay suggested that marine viruses may influence global climate.
A link to the wonderful book, “Coral Reefs in a Microbial Sea.”
Forest Rohwer’s laboratory website.
The role of a retrovirus in the development of the mammalian placenta.
A bacterial role in snow making, using the commercial product “Snomax.”
A “faculty spotlight” essay on Dr. Silveiro.
Dr. Silveiro’s laboratory website.
Dr. Silveiro’s faculty website.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #57: Pitting Metabolic Inhibitors Against Viruses Sep 19, 2024

Matters Microbial #57: Pitting Metabolic Inhibitors Against Viruses September 18, 2024

Today, Dr. Tracie Delgado of the Biology Department at Seattle Pacific University joins the #QualityQuorum to discuss her undergraduate research team’s explorations of how some herpesviruses can cause cancer . . . and how to use the host cell’s metabolism to fight those viruses!

Host: Mark O. Martin

Guest: Tracie Delgado

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Links for this episode

An overview of the herpesviruses as a group.
A description of gammaherpesvirus, the type of herpesvirus with which Dr. Delagado and colleagues work.
The relationship between some herpesviruses and cancer.
The mysterious Warburg Effect, discussed by Dr. Delgado today.
A wonderful TED talk by Dr. Delgado.
A talk Dr. Delgado gave at a 2017 March for Science Event, arguing for more and better representation in STEM.
An article about Dr. Delgado’s journey to science.
Dr, Delgado’s research team’s website with links to research articles that were discussed.
Dr. Delgado’s faculty website.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #56: Marine Microbial Echoes of Evolution Sep 12, 2024

Matters Microbial #56: Marine Microbial Echoes of Evolution September 11, 2024

Today, Dr. Carolina Martinez Gutierrez of the Department of Earth Science at the University of California Santa Barbara joins the #QualityQuorum to discuss her research team’s efforts to unravel how ancient microbes thrived in the early oceans of Earth’s history . . . and to sing the praises of marine microbiology!

Host: Mark O. Martin

Guest: Carolina Martinez Gutierrez

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Links for this episode

An overview of the microbiome of the ocean and geochemistry.
A description of likely conditions on Ancient Earth.
An essay about the Great Oxidation Event—the event that changed our entire planet.
An article by Dr. Martinez Gutierrez and colleagues discussing how phylogenomics can help dissect microbial evolution without fossils.
An overview of Prochlorococcus, one of the microbes Dr. Martinez Gutierrez discussed.
A wonderful video about Prochlorococcus and a remarkable scientist.
An overview of Pelagibacteri ubique (SAR11), one of the microbes Dr. Martinez Gutierrez discussed. An article about the work of Dr. Martinez Gutierrez and her research interests while a postdoctoral scholar
The departmental website for Dr. Martinez Gutierrez
The laboratory website for Dr. Martinez Gutierrez’s research group.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #55: An accidental microbiologist Sep 05, 2024

Today, the award winning and affable Dr. David Westenberg of the Missouri University of Science and Technology joins the #QualityQuorum to discuss his efforts at microbial outreach from K-12 (and beyond), his fascinating research program, and his experiences teaching microbiology to engineers.

Host: Mark O. Martin

Guest: David Westenberg

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Links for this episode

A TEDX talk by Dr. Westenberg.
An overview of the BioBuilder program.
An overview of the iGEM program.
Dr. Westenberg’s page on the Howard Hughes Medical Institute Biointeractive website.
An article about “agar art” with microbes, featuring Dr. Westenberg.
An article about the Woods Hole Microbial Diversity course by Dr. Westerfield.
An article that shows Dr. Westernberg’s approach to teaching in a fun and accessible manner.
Dr. Westenberg’s faculty website.
Dr. Westeinberg’s laboratory group website

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #54: In the shadow of giant viruses Aug 29, 2024

Today, Dr. Mohammad Moniruzzaman, Assistant Professor at the Rosenstiel School of Marine, Atmospheric, and Earth Science at the University of Miami joins the #QualityQuorum to discuss his laboratory group’s work investigating a remarkable group of giant viruses and how they can shape marine algal community structure.

Host: Mark O. Martin

Guest: Mohammad Moniruzzaman

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Links for this episode

Here is a recent review of the giant viruses (more information appears almost monthly!).
Another overview of giant viruses.
An even more recent review of the giant viruses.
An article exploring what we do not know about giant viruses.
A video about giant viruses.
An interesting article relating giant viruses to early cellular evolution.
An article exploring the involvement of giant viruses in the evolution of the eukaryotic nucleus?
A report of endogenous giant viruses making their own genomes part of marine green algae.
The preprint of an article discussed by Dr. Moniruzzaman.
An article about finding giant viruses in very hostile underwater brine pools—the giant viruses are ubiquitous!
An article about Dr. Moniruzzaman’s research.
A video by Dr. Moniruzzaman.
Dr. Moniruzzaman’s faculty website.
Dr. Moniruzzaman’s research laboratory website

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #53: Heavy metal microbes! Aug 22, 2024

Today, Dr. Jennifer Goff of the Department of Chemistry at SUNY College of Environmental Science and Forestry joins the #QualityQuorum to discuss her laboratory’s work studying the relationship between microbes in metal, as well as her path in the microbial sciences.

Host: Mark O. Martin

Guest: Jennifer Goff

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Links for this episode

A fine remembrance of Carl Woese from the journal Nature.
A wonderful book by the great David Quammen that emphasizes the impact Carl Woese had on biology.
An article by yours truly on the impact Carl Woese has on my students.
An overview of biogeochemistry.
The carbon cycle and how the microbial world is involved with the process.
The nitrogen cycle and how the microbial world is involved with the process.
An article about tellurium and microbes.
An older overview of how microbes are involved in mining, as well as a more recent article on that topic.
A review of metals and microbes.
Dr. Goff’s faculty website.
Dr. Goff’s fascinating laboratory group website, including links to the papers discussed by Dr. Goff.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #52: A relationship between the microbiome and nasopharyngeal cancer? Aug 15, 2024

Today, Dr. Justine Debelius of the Johns Hopkins Bloomberg School of Public Health joins the #QualityQuorum to discuss her fascinating work relating the human microbiome to nasopharyngeal cancer, as well as her path in the microbial sciences.

Host: Mark O. Martin

Guest: Justine Debelius

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Links for this episode

A video overview of the human microbiome for introductory MIcronauts.
Another interesting video introduction to the human microbiome.
A review article describing relationships between microbiome and disease in general.
A review article describing possible links between the microbiome and some forms of cancer.
A short video describing possible links between the microbiome and some forms of cancer.
An overview of nasopharyngeal cancer.
A link to the article by Dr. Debelius on the relationship between the microbiome and NPC.
Some updated information on this relationship.
Dr. Debelius’ faculty scientist website.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #51: From Legionella to mentoring to outreach Aug 08, 2024

Today, Dr. Michele Swanson, Professor of Microbiology at the University of Michigan, joins the #QualityQuorum to discuss the her journey to microbiology, the mysterious disease causing bacterium Legionella, and how to best create a better scientific ecosystem.

Host: Mark O. Martin

Guest: Michele Swanson

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Links for this episode

An overview of Legionella and its ability to cause disease from the Centers for Disease Control.
A more formal overview of Legionella and Legionnaire’s Disease.
An overview of Legionella as an interesting microbe.
A review article by Dr. Swanson and colleagues about Legionella.
A review article by Dr. Swanson and colleagues about Legionella’s life cycle.
A history of Legionnaire’s Disease.
An article about the Flint, Michigan outbreak of Legionella related disease.
An article describing how Legionella can use amoebae as hosts, and how that can relate to disease.
An article by Dr. Swanson and colleagues about the Flint, Michigan outbreak of Legionella.
A link to the NIH Advisory Committee to the Director Working Group on Re-envisioning NIH-supported Postdoctoral Training, Dec 2023
The Frontline “Flint’s Deadly Water” documentary.
A link to the NASEM’s 2020 report “Management of Legionella in Water Systems”
A video interview with Dr. Swanson.
Dr. Swanson’s faculty page.
Dr. Swanson’s laboratory page.
Dr. Swanson’s Wikipedia page.
Dr. Swanson coauthored a fine textbook on microbiology.
Dr. Swanson is a cohost on the This Week in Microbiology podcast.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #50: One versus many, the evolution of multicellularity Aug 02, 2024

Today, Dr. Will Ratcliff of the Georgia Institute of Technology joins the #QualityQuorum to discuss the fascinating work his group has done exploring the evolution of multicellularity, and the wonderful example of “snowflake yeast.”

Host: Mark O. Martin

Guest: William Ratcliff

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Links for this episode

A video of a #LuxArt workshop that Dr. Jennifer Quinn and I organized at an ASMCUE conference a few years ago. Such creativity!
Here is a nice editorial overview of the issue of the evolution of multicellular versus unicellular life and how the latter could lead to the former.
Here is a review essay on the topic of the evolution of multicellularity from Dr. Ratcliff’s laboratory group.
A very recent and interesting review article exploring the possible “black swan” event leading to multicellularity in evolution.
A foundational journal article on snowflake yeast from Dr. Ratcliff and research colleagues.
A nice video of the snowflake yeast described by Dr. Ratcliff.
A wonderful ‘must read” essay on the topic of snowflake yeast from Quanta magazine.
A wonderful ‘must read” essay on the topic evolving multicellularity from Quanta magazine.
A wonderful ‘must read” essay about the possibility of multicellular prokaryotes from Quanta magazine.
A really engaging video about the evolution of snowflake yeast from Dr. Ratcliff.
Dr. Ratcliff’s faculty website.
Dr. Ratcliff’s quite fascinating laboratory website. A must read!
Dr. Ratcliff’s outreach website. Another must read!

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #49: Microbes and Macrobes: Always Interconnected Jul 25, 2024

Today, Dr. Margaret McFall-Ngai of the California Institute of Technology, joins the #QualityQuorum to discuss her philosophy of the future of biology. Dr. McFall-Ngai has been described as “…a recognized thought leader regarding the cornerstone role microbiology plays in the life sciences.” I could not agree more.

Host: Mark O. Martin

Guest: Margaret McFall-Ngai

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Links for this episode

For beginning #Micronauts, I suggest this overview of the amazing roles microbes play in the lives of animals and plants: “We are living in a bacterial world, and it’s impacting us more than previously thought“.
Here is the more advanced article coauthored by Dr.McFall-Ngai on this topic: “Animals in a Bacterial World.” A must read.
A video on this topic by Dr. McFall-Ngai.
Another video on this topic by Dr. McFall-Ngai.
A wonderful review of the squid-Vibrio symbiosis (relevant to discussion) from the laboratory of Dr. Karen Visick.
The TCT story: how the same signal creates a light organ in squid and disease in humans.
PAMPs versus MAMPs as a paradigm shift.
A wonderful profile on Dr. McFall-Ngai
An essay about career building by Dr. McFall-Ngai.
Margaret McFall-Ngai’s faculty website.
The McFall-Ngai laboratory website.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #48: Many are bright but few are chosen Jul 18, 2024

Today, Dr. Mark Mandel, Professor of Medical Microbiology & Immunology at University of Wisconsin-Madison, joins the #QualityQuorum to discuss the research his laboratory group does exploring how the luminous bacterium Vibrio fischeri finds its way into its symbiotic partner, the Hawai’ian Bobtail squid Euprymna scolopes. It will be an enlightening podcast!

Host: Mark O. Martin

Guest: Mark Mandel

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Links for this episode

A video for introductory #Micronauts about the squid-Vibrio symbiosis featuring science journalist Ed Yong and two founders of the field, Dr. Ned Ruby and Dr. Margaret McFall-Ngai.
An engaging video about Euprymna scolopes, the larger partner in this symbiosis, described by Dr. McFall-Ngai.
A more advanced overview to this field, authored by Dr. Ned Ruby, Dr. Eric Stabb, and Dr. Karen Visick.
A very complete recent review of the field from Dr. Visick’s lab.
A video presentation by Dr. Mandel about this symbiosis.
The first paper discussed by Dr. Mandel: “Hybrid Histidine Kinase BinK Represses Vibrio fischeri Biofilm Signaling at Multiple Developmental Stages.”
The second paper discussed by Dr. Mandel: “High Levels of Cyclic Diguanylate Interfere with Beneficial Bacterial Colonization.”
The third paper discussed by Dr. Mandel: “Mobile-CRISPRi as a powerful tool for modulating Vibrio gene expression.”
Dr. Mandel’s faculty website.
Dr. Mandel’s laboratory website

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #47: A lifetime enamored with microbes Jul 11, 2024

Today, Dr. Roberto Kolter, Emeritus Professor of Microbiology at Harvard University (and past President of the American Society for Microbiology), joins the Quality Quorum to discuss his life long interest in microbes and microbiology, and how best to present microbiology to the public.

Host: Mark O. Martin

Guest: Roberto Kolter

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Links for this episode

A wonderful article about the complexities of how microbes look and grow with live graphics. I use this article with my introductory #Micronauts every Fall. Beautiful!
An article by Dr. Kolter discussing how to choose a study problem in microbiology…and other areas.
The book “Life at the Edge of Sight” by Dr. Roberto Kolter and Dr. Scott Chimileski is very much worth your time. Highly recommended.
Dr. Scott Chimileski’s website, with beautiful photographs of bacterial colonies.
An article on the history of microbiology by Dr. Kolter.
The article by Dr. Kolter I discussed during the podcast, “Biofilms in lab and nature: a molecular geneticist’s voyage to microbial ecology.”
A lecture by Dr. Kolter and Dr. Chimileski at Harvard University Museum of Natural History.
Another lecture at the Harvard University Museum of Natural History by Dr. Kolter and Dr. Chimileski.
Images from the “World in a Drop Exhibition” can be found here.
An essay from “Small Things Considered” on abortive transduction, discussed in the podcast. Here is another essay on that topic.
A biography of Dr. Kolter.
Dr. Kolter’s laboratory website with many interesting links.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #46: Parsley, Sage, Cholera, and Thyme with Nkrumah Grant Jul 04, 2024

Today, Dr. Nkrumah Grant, Assistant Professor of Microbiology at the University of Illinois at Urbana-Champaign, joins the Quality Quorum today to discuss aspects of his work in bacterial evolution, the challenges of setting up a new research laboratory, and his quite inspiring journey in academia.

Host: Mark O. Martin

Guest: Nkrumah Grant

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Links for this episode

The long term evolution LTEE program by Rich Lenski and his colleagues, studying bacterial evolution in E. coli.
Rich Lenski’s website.
An enjoyable video about this program.
A wonderful explainer of the LTEE program for beginning Micronauts.
Cholera as a disease.
Vibrio cholera the bacterium.
Mechanisms of the cholera toxin.
An article about Vibrio cholera, chitin, and natural transformation.
Rita Colwell, and her research showing how filtering through sari cloth could reduce the incidence of cholera. Here is an overview for new Micronauts.
Chris Waters’ laboratory website at Michigan State University.
An overview from the American Society for Microbiology, suggesting that many food items are in fact antimicrobial.
A review article on the topic of antimicrobial components of food.
A preprint of Dr. Grant’s research that was discussed during the podcast.
An inspirational video of Dr. Grant’s path through science.
Another video about Dr. Grant’s life.
An article about Dr. Grant’s story.
An article by Dr. Grant’s institution, welcoming him to Urbana, Illinois.
Dr. Grant’s faculty page at the University of Illinois at Urbana-Champaign.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #45: CU Later Microbes: Copper as an Antimicrobial Agent! Jun 27, 2024

Today, Dr. Michael Schmidt of This Week in Microbiology and Professor of Microbiology and Immunology of the Medical University of South Carolina, joins the Quality Quorum (at a special “live audience” podcast session at the American Society for Microbiology in Atlanta, Georgia) to discuss his fascinating work with copper as an antimicrobial agent.

Host: Mark O. Martin

Guest: Michael Schmidt

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Links for this episode

An overview about antimicrobial copper.
An article about the mechanism by which copper metal destroys bacteria and viruses.
A review article about the use of copper metal to reduce disease transmission in hospitals.
Here is an older YouTube video by Dr. Schmidt about the use of antimicrobial copper.
A news story about Dr. Schmidt’s work with copper and disease causing organisms in hospitals.
A recent article on this topic by Dr. Schmidt and colleagues.
The faculty website for Dr. Schmidt.
The laboratory website for Dr. Schmidt (with many excellent references on this topic to peruse).

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #44: Labs, Labs, Congress, and Classrooms! Jun 21, 2024

Today, Dr. Kimberly Walker, Assistant Professor and Director of Medical Diagnostics at the University of Delaware, joins the #QualityQuorum to discuss her interesting path in microbiology, from pathogenic bacteria, to predatory microbes, to Congress, to science policy, and then to educating others about medical diagnostics.

Host: Mark O. Martin

Guest: Kimberly Walker

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Links for this episode

An article about the wonderful Microbial Diversity Course put on by the Marine Biological Laboratories at Woods Hole Massachusetts.
The website for the Microbial diversity course. Is it not beyond merely awesome?
An essay I wrote about the late Dr. Abigail Salyers.
An essay I wrote about the late Dr. Edward Leadbetter.
An article on the value of mentorship in general and the challenges to be faced. If you would like to dig deeper, here is an entire book on the vital subject.
An overview about Medical Laboratory careers.
Here is a link to the Congressional Science Fellows program, for which Dr. Walker was an aide to the late Senator Paul Wellstone of Minnesota.
Here is the website for Dr. Alison Weiss, Dr. Walker’s PhD advisor, who was a wonderful mentor.
Here is the website for Dr. Henry Williams, who was another fabulous mentor to Dr. Walker.
Here is a link to the forensics lab for which Dr. Walker was on the Advisory Board.
A link to Lorain County Community College, where Dr. Walker ran the MLT and Phebotomy program.
A link to the University of Maryland Department of Medical and Research Technology, where Dr. Walker earned her degree and worked for ten years.
Dr. Walker’s faculty website.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #43: New Archaea from old habitats Jun 06, 2024

Today, Dr. Roland Hatzenpichler of Montana State University joins the #QualityQuorum to discuss the central importance of archaea to our knowledge of the microbial world, ranging from history of their study, misconceptions about archaea, the microbiological bounty of Yellowstone National Park, and how ancient archaea may be the Asgard like ancestors of us all.

Host: Mark O. Martin

Guest: Roland Hatzenpichler

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Links for this episode

A solid video describing the archaea.
A wonderful if dated (ASM, you need to make an updated version) video about the contributions of Carl Woese to the description of the archaea.
An essay by yours truly about Carl Woese (and the only time I will EVER be published in the journal RNA Biology.)
A more solid essay about Carl Woese.
A MUST READ article by Ed Yong on the role that Norm Pace has played in understanding the microbial world.
An article about the role Yellowstone National Park has played in microbiology.
An article about the wonderful “underwater oasis” called “Asgard.”
A wonderful article by Ed Yong about what could be our remote ancestors, the Lokiarcheota.
The first paper that was mentioned: Carl Woese’s discovery of the archaea.
From the second group of articles that were mentioned: archaea are everywhere.
From the third group of articles that were mentioned: archaea drive biogeochemical cycles.
From the fourth group of articles that were mentioned: Lokiarcheota may bridge the gap between prokaryote and eukaryote.
A video on extremophiles from Dr. Hatzenpichler.
Dr. Hatzenpichler’s faculty profile.
Dr. Hatzenpichler’s quite wonderful laboratory website.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #42: Many paths to microbiology with Jessica Buchser May 30, 2024

Today, Jessica Buchser, graduate of West Chester University and entering PhD student at Pennsylvania State University joins the #QualityQuorum to discuss being an older student, how social media and podcasts fueled her interest in the microbial sciences, and her future path as a microbiologist!

Host: Mark O. Martin

Guest: Jessica Buchser

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Links for this episode

The video that Dr. Jennifer Quinn and yours truly did for Harvard University’s Microbial Science Initiative this April.
A link to the Microbial Science Initiative.
An overview of scanning electron microscopy (SEM).
Website for West Chester University’s Biology Department, where Jess Buchser just earned her undergraduate degree.
The website of Dr. John Pisciotta, one of Jess Buchser’s mentors at West Chester University.
The website of Dr. Manu Ramalho, one of Jess Buchser’s mentors at West Chester University (an prior podcast guest for #MattersMicrobial episode #32).
The website of Dr. Seth Bordenstein, who will be Jess Bucher’s PhD advisor at Pennsylvania State University in the Fall (and also a prior podcast guest for #MattersMicrobial episode #3).
An essay on the importance of mentors and mentorship in the microbial sciences.
Useful resources for older and nontraditional undergraduate students in STEM fields. Here is another essay on this topic.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #41: Giant Bacteria: Not All Are Small! with Esther Angert May 23, 2024

Today, Dr. Esther Angert of Cornell University joins the #QualityQuorum to discuss the role her research collaborators have had studying truly gigantic bacteria, and the adaptations these enormous microbes must make to their size!

Host: Mark O. Martin

Guest: Esther Angert

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Links for this episode

A video describing the surface area versus volume problem in biology.
A wonderful introductory essay on sizes of bacteria…both big and small.
An older review article on giant bacteria.
A more recent review article on giant bacteria.
A video about Epulopiscium.
An essay about Epulopiscium.
An overview of Epulopiscium by Dr. Angert.
A recent research article on Epulopiscium from Dr. Angert’s research group.
An essay about Thiomargarita namibiensis.
An essay about Achromatium, another giant microbe.
An essay about the current most mammoth microbe, Thiomargarita magnifica
A more scientific article on Thiomargarita magnifica with Dr. Angert as co-author.
Dr. Angert’s faculty and administrative website.
Dr. Angert’s truly wonderful laboratory website.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #40: Using THOR's hammer to investigate microbial communities May 16, 2024

Today, Dr. Jo Handelsman of the University of Wisconsin Madison and Director of the Wisconsin Institute for Discovery joins the #QualityQuorum to discuss the work she and her research collaborators do on interactive microbial communities, using THOR (the hitchhikers of the rhizosphere) as a model system. She will also remind us how vital soil is to our lives.

Host: Mark O. Martin

Guest: Jo Handlesman

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Links for this episode

An article on the story of “uranium glass,” that fluoresces under ultraviolet light. Here is another interesting article on the topic.
The website for Hartiful, who makes custom enamel pins (including some that glow in the dark, as all cool things should).
Giant Microbes makes small and large plush toys of microbes and other biology related items.
An overview of ice nucleation proteins. Here is a more technical article on the topic.
The story of SNOWMAX.
Ice nucleation proteins and snowflakes.
One of my favorite videos from my microbiology class in 2008, demonstrating ice nucleation by Pseudomonas syringae.
The website for the Tiny Earth antibiotic crowdsourcing CURE.
The website for Dr. Handelsman’s book, “A World Without Soil.”
An explainer of THOR, for new micronauts.
A technical publication from Dr. Handelsman’s research group on THOR.
An explainer of microbial “zorbs,” for new micronauts.
A technical publication from Dr. Handelsman’s research group on “zorbs.”
Dr. Handelsman’s page on Wikipedia.
Dr. Handelsman’s faculty page.
Dr. Handelsman’s research website.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #39: Global flatulence: Mysterious Archaea and methane May 09, 2024

Today, Dr. Geo Santiago-Martinez, Assistant Professor of Molecular and Cell Biology and Microbiology at the University of Connecticut joins the #QualityQuorum to discuss the mysteries of the archaeal world, and how one group of these organisms produce methane gas as a byproduct of metabolism. These methanogens are thus involved in climate, symbioses, biotechnology, and even astrobiology!

Host: Mark O. Martin

Guest: Geo Santiago-Martinez

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Links for this episode

An essay about how cyanobacteria changed our very planet.
A truly wonderful and highly recommended video about Leeuwenhoek and how he was the first to “see through microbial eyes.” PLEASE WATCH THIS AMAZING VIDEO!.
A link to the Boerhaave Museum in Amsterdam (well worth the visit!) including how to obtain a replica of the Leeuwenhoek microscope (*I* do not have one—they are awesome!).
A video overview of the archaea.
A review article on the archaea.
Haloquadratum walsbyi: a square archaean.
Pyrodictium abyssi: a netlike organism.
The process of methanogenesis by archaea (focused on the gut).
An essay describing how methanogenic archaea may impact climate change.
The famous Volta experiment!
An article on Methanosarcina acetivorans, studied by Dr. Santiago-Martinez and his coworkers.
A very interesting article on methanogenesis by Dr. Santiago-Martinez.
A wonderful video of Dr. Santiago-Martinez and his collaborators’ research.
The Archaea Power Hour website.
The Cientifico Latino website, increasing diversity within STEM.
Dr. Santiago-Martinez’s faculty website.
Dr. Santiago-Martinez’s laboratory website.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #38: Microbes, cheese, and Brie-ond! May 02, 2024

Today, Dr. Rachel Dutton, Science Resident at the Astera Institute in Berkeley, California, joins the #QualityQuorum to discuss the complex (and tasty) microbial communities responsible for cheese as a model system for microbial interactions, as well as her interesting path through science.

Host: Mark O. Martin

Guest: Rachel Dutton

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Links for this episode

An introduction to the idea of sociomicrobiology.
A more technical review of sociomicrobiology.
Another more recent technical review of sociomicrobiology.
A popular introduction to the ideas behind microbiology and cheesemaking.
An article about cheese microbes.
An article about viewing fermented foods like cheese as a way to study microbial ecosystems.
Evidence for horizontal gene transfer within cheese microbial communities.
A wonderful video about cheese microbiology.
A video by Dr. Dutton about her work in cheese microbiology.
A more recent (2023) video from Dr. Dutton about her cheese community research.
Dr. Dutton’s website on cheese microbiology.
Dr. Ben Wolfe’s website on cheese microbiology.
A podcast with Dr. Dutton from ASM.
A popular article about Dr. Dutton’s work with cheese microbiology.
Dr. Dutton’s Wikipedia page!
An overview of Arcadia Science.
An overview of the Astera Institute.
Dr. Dutton’s site at Astera.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #37: Wolbachia and STEM: Two symbioses! Apr 25, 2024

Today, Sarah Bordenstein, Associate Research Professor of Biology & Entomology at Penn State University and Director of Discover the Microbes Within! The Wolbachia Project joins the #QualityQuorum to tell us about the most successful pandemic on the planet, the fascinating endosymbiotic bacterium Wolbachia, and how she has used this fascinating system to teach young people about molecular biology, bioinformatics, and evolution.

Host: Mark O. Martin

Guest: Sarah Bordenstein

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Links for this episode

An overview about trilobites.
The story of Beecher’s Quarry.
An article about the fine work of Markus Martin.
The microbially influenced glass art of Jane Hartman.
An overview of metagenomics as a scientific field.
An article about finding antibiotic resistance genes in unexpected places.
A popular article on Wolbachia by Ed Yong
Another popular article on Wolbachia, describing the effects on their host.
A more scientific review about Wolbachia.
A quick video overview of the program that Professor Bordenstein and colleagues use to teach about Wolbachia and STEM.
The “Wolbachia Project” website.
The “Wolbachia Project Database” website.
The Bordenstein Laboratory website.
A prestigious award to Professor Bordenstein.
Sarah Bordenstein’s faculty website at Penn State

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #36: Leafy microbial strangers with benefits Apr 18, 2024

Today, Dr. Jeri Barak of the University of Wisconsin Madison joins the #QualityQuorum to chat about how various microbes (some of which can cause disease in humans) can gain access to plants, sometimes via group behavior. With media coverage of Salmonella contamination in lettuce, Dr. Barak’s work is especially timely! She will also discuss what it is like to be a plant pathologist!

Host: Mark O. Martin

Guest: Jeri Barak

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Links for this episode

An overview of ammonite fossils.
An article about the amazing glowing petunia. And here is a second popular article on the Firefly Petunia. Finally, here is a more scientific article describing this achievement.
An overview of produce contamination by Salmonella and other pathogens. Here is another article worth your time.
An overview of pathogens to be found in the environment.
CDC guidelines and information about bacterial contamination of produce.
An absolutely fabulous overview of some of the work done in Dr. Barak’s lab discussed during this episode. It is a wonderful science-communication with art essay. A must read for any interest level!
A article by Dr. Barak’s group describing how a plant infection can allow human pathogens to proliferate inside of a plant.
Dr. Barak’s faculty website.
Dr. Barak’s laboratory website.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #35: Clostridioides difficile: From Bench to Bedside and Back Again Apr 12, 2024

Today, Dr. Vincent Young of the University of Michigan Department of Internal Medicine and Infectious Disease Division in Ann Arbor, joins the #QualityQuorum to chat about the ecology of the human gut as it relates to a serious bacterial disease caused by Clostridiodes difficile. He will also discuss what it is like to be a medical scientist with both MD and PhD degrees.

Host: Mark O. Martin

Guest: Vincent Young

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Links for this episode

Backyard DNA sequencing—is this a possibility? Here is a source of information. And Sebastian Cocioba is a great source of information.
The company Giant Microbes makes a C. diff plush toy.
An introduction to C. difficile the bacterium.
An introduction to the disease caused by C. difficile.
Some journal articles by Dr. Young and his colleagues and discussed in this podcast: “Viewing Bacterial Colonization through the Lens of Systems Biology,” “Capturing the environment of the Clostridioides difficile infection cycle,” “Microbiome therapeutics for the treatment of recurrent Clostridioides difficile infection,” and “Longitudinal genomic surveillance ofcarriage and transmission of Clostridioides difficile in an intensive care unit.”
Dr. Young’s colleague Dr. Madeline Barron, who writes wonderful essays about microbiology for the American Society for Microbiology.
An informative interview with Dr. Young. Here is another good interview.
A good biography of Dr. Young from ASM.
Dr. Young’s faculty website.
Dr. Young’s laboratory website.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #34: Artificial gut feelings: Gut microbes and the ECM Apr 04, 2024

Today, Dr. Ana Maria Porras of the Department of Biomedical Engineering at the University of Florida, joins the #QualityQuorum to chat about her work studying gut microbes and the gut, IBDs, representation, and even how fiber arts can inspire microbial wonder!

Host: Mark O. Martin

Guest: Ana Maria Porras

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Links for this episode

The announcement of Dr. Porras’ prestigious CAREER grant from the National Science Foundation.
A basic introduction to irritable bowel syndrome.
An overview of irritable bowel syndrome (IBS).
An article about “remodeling” of the gut epithelia during IBS.
The journal article from Dr. Porras’ research group discussed in today’s podcast.
A video by Dr. Porras about her research.
A video by Dr. Porras about her microbial outreach using fabric arts, as well as an article on that topic.
Instructions from Dr. Porras describing how to crochet a microbe of your own!
Dr. Porras’ faculty website.
Dr. Porras’ laboratory website.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #33: Ancient Fats in Modern Microbes with Paula Welander Mar 28, 2024

Today, Dr. Paula Welander, Associate Professor of Environmental Earth System Science at Stanford University (and #DocMartian #4) joins the #QualityQuorum to discuss the work she and her colleagues are doing probing at early life by studying lipid biosignatures that can appear in the fossil record—and the role that cholesterol and related molecules have on microbial life.

Host: Mark O. Martin

Guest: Paula Welander

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Links for this episode

A blog post I wrote about the truly remarkable late Dr. Abigail Salyers, who taught me the importance of being authentic as a scientist, educator, and human being.
An essay about the Great Oxidation Event early in our planet’s history.
Information about BIFs—banded iron formations.
An overview of stromatolites, both popular and scholarly.
The Gunflint stromatolites.
The story of WIlliam Schopf and stromatolites.
The fluid mosaic model of cell membranes.
The role of cholesterol in membranes.
A nice description of some of Dr. Welander’s work with hopanoids.
Hopanoids in cyanobacterial membranes.
An overview of biosignatures relevant to geobiology.
The cell membrane and other differences of archaea.
Adaptations to hyperthermophily in archaea and bacteria.
The “Echoes of Life” book mentioned in the podcast.
A fascinating article by Jo Handelsman and coauthors about implicit and unconscious bias in science. Here is an update on this work, and a video presentation.
A really interesting video interview with Dr. Welander.
Dr. Welander’s departmental/divisional website.
Dr. Welander’s laboratory website

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #32: What's bugging ants, microbially speaking? Mar 21, 2024

Today, Dr. Manu Ramalho of West Chester University in Pennsylvania joins the #QualityQuorum to discuss the wonderful world of ants, their microbiomes, and what their intersection can teach us about our place in the natural world.

Host: Mark O. Martin

Guest: Manu Ramalho

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Links for this episode

I wear some microbial themed ties made by Michele Banks of Artologica. Both Michele and Vexed Muddler understand #MicrobialArt.
One of the #LuxArt sessions that I conducted at an ASMCUE session a few years ago. Dr. Quinn and I would love to do more sessions!
Pi Day is an important mathematical holiday.
Dr. Jennifer Quinn at the University of Washington – Tacoma, proud member of the Mathematics Association of America, and on Wikipedia!
Albert Einstein’s birthday.
The quite amusing 1950s movie about “giant ants,” titled “Them!”
A review of Paul Buchner’s encyclopedic work on endosymbiosis. Some day, I will own a copy of this book!
A wonderful book describing microbial symbionts of insects, titled “Influential Passengers.”
A review of insects and endosymbionts.
Nutritional endosymbiosis in insects.
A review of Wolbachia.
When Wolbachia creates plant hormones to provide food for its insect hosts.
The website for “Discover the Microbes Within” which is a CURE based student sourced investigation of Wolbachia in arthropods. It was designed by Seth Bordenstein and Sarah Bordenstein.
An introduction to leaf cutter ants. Video.
An overview of the leaf cutter ant microbiome.
A very relevant article coauthored by Dr. Ramalho describing the relationship between turtle ants and their microbiome.
An interesting video interview with Dr. Ramalho.
Dr. Ramalho’s faculty website.
Dr. Ramalho’s laboratory website.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #31: Spirochetes do things...differently Mar 14, 2024

Today, Dr. Brian Stevenson of the University of Kentucky College of Medicine joins the #QualityQuorum to discuss a twisty twirling form of life, spirochetes, ticks, and human diseases like Lyme Disease.

Host: Mark O. Martin

Guest: Brian Stevenson

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Links for this episode

The Latin Translator I have used (because if I am getting it tattoo’ed, I want it to be correct).
The custom enamel pins of Hartiful.
An overview of spirochetes in general.
A review of spirochete motility.
The strange world of ticks and spirochetes.
A review of Lyme disease.
A “House” episode involving Borrelia.
A wonderful review article by Dr. Stevenson.
Dr. Stevenson’s faculty website.
Dr. Stevenson’s laboratory website

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #30: Deep (Marine Microbial) Thoughts with Jennifer Biddle Mar 01, 2024

Today, Dr. Jennifer Biddle of the School of Marine Science and Policy at the University of Delaware joins the #QualityQuorum to discuss deep microbial life in marine environments (and why you should care about it), as well as her fascination with archaea!

Host: Mark O. Martin

Guest: Jennifer Biddle

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Links for this episode

The Tiny Earth program website, originated by Dr. Jo Handelsman.
A review of the marine archaea.
An article about microbial diversity in marine sediments.
An article on methane and deep microbial sediments.
A nice blog post about sulfur oxidizing microbes in marine sediments.
Work by Dr. Biddle and colleagues on hydrogen consuming bacteria in deep sediments.
Work by Dr. Biddle and colleagues on geochemical processes promoting microbial growth in deep marine sediments..
The wonderfully strange skeleton shrimp discussed by Dr. Biddle.
A video explaining about taking a dive on the marine submersible Alvin.
Dr. Biddle’s faculty website at the University of Delaware.
Dr. Biddle’s laboratory website.
The forgotten woman who made microbiology possible

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #29: Exploring cave microbiology and career paths with Hazel Barton Feb 23, 2024

Today, Dr. Hazel Barton, Loper Endowed Professor of Geological Sciences at the University of Alabama, joins the #QualityQuorum to tell us about her explorations of cave microbiology and the relationship between microbiology and geology!

Host: Mark O. Martin

Guest: Hazel Barton

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Links for this episode

An introduction of the fascinating field of geomicrobiology.
An recent introduction to cave microbiology.
An overview of Lechuguilla Cave discussed by Dr. Barton.
An overview of Carlsbad Caverns discussed by Dr. Barton.
An overview of Deer Cave in Borneo discussed by Dr. Barton.
An overview of Wind Cave discussed by Dr. Barton.
An article from Dr. Barton’s lab describing antibiotic resistance genes among cave microbes.
An article from Dr. Barton and colleagues suggesting that iron metabolism could lead to cave formation.
An article from the Barton lab describing microbial photosynthesis driven by far red light in caverns.
An article from Dr. Barton and colleagues describing the very unusual low bioload/high diversity microbial communities deep within Wind Cave.
Dr. Barton’s faculty page at the University of Alabama.
Dr. Barton’s quite impressive website about cave microbiology.
A very impressive video with Dr. Barton.
A fun “Twenty Questions” video with Dr. Barton.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #28: From Lizard Cloacal Microbes to CPG in the Business Sector with Franny Gilman Feb 16, 2024

Today, Dr. Franny Gilman, Principal Scientist at the Kraft-Heinz Company (and another #DocMartian who worked in my undergraduate research lab), joins the #QualityQuorum to tell us about the path that took her from studying the cloacal microbiome of lizards to Greenland and eventually to food science!

Host: Mark O. Martin

Guest: Franny Gilman

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Links for this episode

The paper that first caught Dr. Gilman’s eye when I suggested she read it while in my laboratory: “The influence of sex, handedness, and washing on the diversity of hand surface bacteria.”
Another paper suggested by Dr. Gilman: “Boomerang academics: why we left academia for industry, but then came back.”
Still another paper: “Academia or Industry: Where Would I Fit In?”
A website for the Institute of Food Technologists, with wonderful links and information.
A nonspecialist’s introduction to Aspergillus oryzae that makes koji.
A review article about the koji mold, Aspergillus oryzae.
A conference website devoted to the study of koji and A. oryzae.
Dr. Gilman’s LinkedIn profile.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #27: Broccoli sprouts, gut health, and microbes for all with Dr. Sue Ishaq Feb 09, 2024

Today, Dr. Sue Ishaq of the University of Maine joins the #QualityQuorum to tell us about the relationship between what we eat and our microbes, as well as making microbiology more inclusive to everyone.

Host: Mark O. Martin

Guest: Sue Ishaq

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Links for this episode

An explanation of Charles Darwin’s quotation about having a bad day.
The laboratory website of Dr. Michael Baym, who sent me that quotation as a metal plate for my lab. Much appreciated!
An article about broccoli metabolism.
An introductory article for the public about broccoli consumption and IBD.
A 2023 article from Dr. Ishaq’s group suggesting a relationship between consuming broccoli sprouts and reduction of inflammatory bowel disease in mice.
A 2023 article https://journals.asm.org/doi/10.1128/msystems.00532-23 from Dr. Ishaq’s group relating the consumption of steamed broccoli sprouts to reduction of inflammation in mice.
A very readable introduction to the concept of microbiology and social equity.
A link to a number of essential articles relating microbiology and social equity—microbiology should be for EVERYONE.
The faculty website of Dr. Ishaq at the University of Maine.
The WONDERFUL laboratory website of Dr. Ishaq.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #26: Cultivating the hidden microbial majority Feb 02, 2024

Today, Dr. Cameron Thrash of the University of Southern California will discuss marine microbiology, an extremely…ubiquitous…microbe (with a name every #Micronaut should know!), conducting research at sea, and his path in science.

Host: Mark O. Martin

Guest: Cameron Thrash

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Links for this episode

Here is an essay describing the Great Plating Anomaly and a criticism of that approach.
A wonderful video (scan forward to 27 minutes in for the relevant part) about the discovery of SAR11.
An interview with Dr. Stephen Giovannoni about marine microbiology.
An introductory overview of Pelagibacter ubique and a more thorough review.
How the genome of Pelagibacter and other small microbes have been “darwinnowed” over time by evolution.
A review article about Pelagibacter and regulation.
Here and here are two examples of Dr. Thrash’s CURE approach with undergraduates.
Here is Cameron Thrash’s faculty website.
Here is Cameron Thrash’s really quite awesome laboratory website.
For indispensable links to myriad fascinating articles about microbiology, check out Cameron Thrash on X (formerly Twitter) (@jcamthrash) and BlueSky (@jcamthrash .bsky.social)

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #25: Gut feelings about phage and the gut microbiome Jan 25, 2024

Today, Dr. Danielle Campbell (and former #DocMartian!), a postdoctoral scholar of the Baldridge group at Washington University in St. Louis, will share her research into the relationship between bacteriophage and the gut microbiome…as well as chat about her path in science.

Host: Mark O. Martin

Guest: Danielle Campbell

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Links for this episode

Here is a link to a wonderful review article by Dr. Campbell describing the role that the microbiome can have on viral infections.
Here is a link to a a publication describing the Salyersviridae, as described by Dr. Campbell.
I wrote an essay about Abigail Salyers here.
Here and here can be found more biographical information about Dr. Salyer’s contribution to microbiology, and the remarkable life she led.
A description of the career changing Microbial Diversity Course at the Marine Biological Laboratory in Woods Hole, Massachusetts.
A link to the Baldrige Laboratory at Washington University of St. Louis, where Dr. Campbell is a postdoctoral scholar.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #24: It takes a quorum to cause disease Jan 18, 2024

Today, Associate Professor of Biology Dr. Julia van Kessel of Indiana University will chat with us about how groups of bacteria can sense one another and carry out behavior as a collective…including some kinds of disease!

Host: Mark O. Martin

Guest: Julia van Kessel

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Links for this episode

An introduction to the horrific disease leprosy, caused by the quite strange organism Mycobacterium leprae.
An overview of the Hansen Institute in Ethiopia.
A solid overview of quorum sensing.
A very interesting review article about quorum sensing.
A video that two of my Bio350 Micronauts (including a former guest of our podcast, Dr. Ruth Isenberg) put together some years ago to illustrate the idea of quorum sensing.
A very clear overview of quorum sensing by the highly energetic and brilliant Dr. Bonnie Bassler, one of the giants of this field.
A #LuxArt show I organized a few years ago at Carleton College, where I encouraged students to create art by “painting” with luminous bacteria on Petri dishes. It is a true merger of art and science.
Using Chromobacterium to “look” for quorum sensing molecules. I made this imperfect video to illustrate the concept.
My old friend Vibrio harveyi, which Dr. van Kessel uses in her laboratory.
Vibrio coralliilyticus, which causes coral diseases.
If you are interested in learning about how some bacteria have what seems to be a molecular switchblade knife—the Type 6 Secretory System— to use against other bacteria or other organisms, the link above is a fine place to start. In addition, a Bio350 student of mine made a lovely Claymation video of the process some years ago.
Here is Dr. van Kessel’s faculty website at Indiana University in Bloomington.
Here is the laboratory website—with excellent graphics and videos—of Dr. van Kessel’s group.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #23: Fungi: Cool Friends and Looming Foes Jan 05, 2024

Today, the impressive Dr. Arturo Casadevall of Johns Hopkins University will joint #MattersMicrobial to discuss his path in science, how fungi need more study, that some fungi are literally cool, and others a looming threat.

Host: Mark O. Martin

Guest: Arturo Casadevall

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Links for this episode

A wonderful remembrance (by multiple authors) of Lynn Margulis, and essays by Elio Schaechter (a friend of Margulis’) and James Lake (a colleague).
The wonderful Tiny Earth program that uses a CURE type approach to allow students to search for new antibiotic producing microbes. Also, a fine publication describing this worldwide program.
An overview of the diverse and dizzying fungal world all around us.
A publication describing how fungi dominated after every mass extinction.
Giant fungi existed in Earth’s past.
Dr. Casadevall group’s article on how fungi are cooler than the environment around them, including the “mycorefrigerator.”
Evidence that high body temperatures defend against fungal disease. Dr. Casadevall wrote an article suggesting that fungal diseases might have helped lead to the extinction of dinosaurs.
Dr. Casadevall explores the possibility of fungal adaptation to higher temperatures in our warming world.
Dr. Casadevall’s essay about problems with the term “pathogen.”
Drs Casadevall and Fang’s new book titled “Thinking About Science.”
A short biography of Dr. Casadevall as well as his Wikipedia page.
Dr. Casadevall’s faculty website

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #22: A microbial path through the graduate school maze with Lauren Augusta Dec 29, 2023

Today my former undergraduate student Lauren Augusta, currently in a PhD program in Microbiology at the University of Indiana, joins the podcast to chat about how she chose her career path in the microbial sciences, and her future path.

Host: Mark O. Martin

Guest: Lauren Augusta

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Links for this episode

The program for creating the maze on this session’s thumbnail image is here.
Here is the website for Micropia, the microbiology museum in Amsterdam in the Netherlands. SO WORTH YOUR TIME. I wish that I worked there!
Here is a description of Micropia’s “tardigrade chair” which is kind of a tourist destination!
Lauren Augusta, today’s guest on the podcast, did a wonderful video advertisement for my institution, the University of Puget Sound.
An introduction for beginning micronauts about Agrobacterium, and why you should care about this natural genetic engineer, as well as a more advanced review. Plus another fine review from Dr. Clay Fuqua and coworkers.
Lovely overviews of the global signaling molecule of bacteria that Lauren studies, cyclic-di-GMP, can be found here, here, and here.
The Microbiology Department website at the University of Indiana where Lauren is working on her Ph.D.
The faculty webpage of Lauren’s Ph.D. supervisor, Dr. Clay Fuqua.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #21: Microbes, mermaids and coral reefs with Chris Kellogg Dec 22, 2023

Today Dr. Christina Kellogg of the USGS St. Petersburg Coastal and Marine Science Center in St. Petersburg Florida chats with the podcast about her many diverse adventures in marine microbial ecology! It’s quite a high energy microbial journey!

Host: Mark O. Martin

Guest: Chris Kellogg

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Links for this episode

The recycled metal artwork of Brian Mock has a website here.
Interested in how bacterial respiration can generate electricity? See this interesting review paper. And with the holidays approaching, you might even make a microbial fuel cell of your own here!
An video introduction to coral reefs
A fine review essay on coral reefs and bacterial diseases.
Very much worth your time: a video (including Dr. Kellogg) describing coral microbiology.
Video from Dr. Kellogg #1: A Deep Sea Coral Expedition.
Video from Dr. Kellogg #2: Coral Disease Projet in Kauai.
Video from Dr. Kellogg #3: DEEP Sea Exploration to Advance Research on Coral/Canyon/Cold Seep Habitats.
Dr. Kellogg’s website is here

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #20: Who You Calling Weird? Diving into Microbes at the Bottom of the Ocean Dec 15, 2023

Matters Microbial #19: You are what you(r microbes) eat Dec 08, 2023

Today Dr. Suzanne Devkota of the Cedars-Sinai Division of Gastronterology and Director of the Cedars Sinai Human Microbiome Research Institute will tell us about the role that our diet plays in the gut microbiome, and how that can impact health. So it really is true: you ARE what you(r microbes) eat!

Host: Mark O. Martin

Guest: Suzanne Devkota

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Links for this episode

An overview for beginning micronauts on diet and the human microbiome, from the Harvard School of Public Health.
A good review article for more experienced micronauts.
A really informative and engaging talk by Dr. Devkota about diet and the microbiome.
An article by Dr. Devkota about using the microbiome to explore health issues.
Another article by Dr. Devkota reviewing how dietary changes can impact the microbiome.
Dr. Devkota’s faculty website.
Dr. Devkota’s excellent laboratory website.
In addition, Dr. Devkota sent along two links: one to an overview of the microbiome institute at Cedars-Sinai, and one about how the Western diet impacts the human microbiome.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #18: The Perfect Predator: Why Phage is Rage Dec 01, 2023

Today Dr. Steffanie Strathdee, Associate Dean of Global Health Sciences at UC San Diego and Co-Director at the Center for Innovative Phage Applications and Therapeutics, will chat with us about how bacteriophages—viruses that attack bacteria—changed her life and are becoming part of our future.

Host: Mark O. Martin

Guest: Steffanie Strathdee

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Links for this episode

A fun video about bacteriophages.
A pretty solid overview about bacteriophages.
An article about the history of bacteriophages.
An article about a truly prophetic book—“Arrowsmith”--- from 1925, by Sinclair Lewis, about using bacteriophages to fight disease.
A wonderful TED talk about the rise of antibiotic resistant pathogens by Maryn McKenna.
A nice overview of ESKAPE pathogens and antimicrobial resistance.
A link to a recent talk given by Dr. Strathdee.
A link to Dr. Strathdee’s recent book, “The Perfect Predator.”
A super recent and quite wonderful review article about phage therapy by Dr. Strathdee.
The SEAPHAGES program (which I always wanted to be part of!!)
Ry Young’s laboratory website.
Dr. Strathdee’s faculty website.
Dr. Strathdee’s Wikipedia page!
A link to the website of the Center for Innovative Phage Applications and Therapeutics (IPATH).

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #17: Evolution in action for everyone with Vaughn Cooper Nov 24, 2023

Today Dr. Vaughn Cooper, Professor in the Department of Microbiology and Molecular Genetics at the University of Pittsburgh, will chat with us about how he and his team teach high school students and undergraduates about evolution occurring in real time—using bacteria.

Host: Mark O. Martin

Guest: Vaughn Cooper

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Links for this episode

The Erg Chech 002 meteorite story, which is fascinating.
The “World Without Microbes” article—highly recommended.
The “World Without Microbes” video—quirky and fun, despite the subject matter.
A solid review of the work of Rich Lenski, as well as his website.
Vaugh Cooper’s faculty website.
Vaughn Cooper’s laboratory website.
Vaughn Cooper’s “Evolving STEM” website.
A wonderful video by Dr. Cooper about Evolving STEM.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #16: What’s bugging the fruit fly microbiome? Nov 17, 2023

Today Dr. Nichole Broderick, Assistant Professor in the Biology Department at Johns Hopkins University, will chat with us about how the study of the fruit fly microbiome can give us insights into human health and disease.

Host: Mark O. Martin

Guest Nichole Broderick

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Links for this episode

The artist “Chocolate Menagerie”’s Etsy site.
Another nice introductory video about the microbiome for new micronauts.
An article describing how the press reports on microbiome-related issues.
A review describing how fruit flies can be good model systems for the study of disease.
Dr. Nichole Broderick’s faculty website.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #15: A Gut Feeling About Precision Medicine Nov 10, 2023

Today Dr. Sean Gibbons, Associate Professor at the Institute for Systems Biology, will chat with us about how the study of host-associated microbial communities can give us insights into evolution, ecology, and even human health.

Host: Mark O. Martin

Guest: Dr. Sean Gibbons

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Links for this episode

A wonderful overview of ammonites, extinct so long ago.
A short biography of the late great Abigail Salyers, and another biography.
My blogpost remembering Abigail and her fine mentorship of yours truly.
A surprisingly solid overview of the microbiome.
A fine video introducing the human microbiome.
An article describing myths and misconceptions about the microbiome.
The wood rat - creosote - microbiome study discussed in today’s session.
An introduction to the question, “What is systems biology?”
The Institute for Systems Biology website.
Sean Gibbons’ faculty page at the Institute for Systems Biology.
Sean Gibbons’ laboratory webpage.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #14: An inordinate fondness for viruses with Jack Gilbert Nov 03, 2023

Today Dr. Jack Gilbert, Professor of Pediatrics and of the Scripps Institution of Oceanography, chats with us about his MANY interests in microbiology, from human health to marine environments.

Host: Mark O. Martin

Guest: Jack Gilbert

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Links for this episode

Marley and Murtle’s Etsy shop, which created my glow in the dark needle felted tardigrade.
My wife Dr. Jennifer Quinn’s Wikipedia page and blog.
Ethan Kocak’s fine artwork is found at his website.
An overview of the BLAST program used for sequence analysis.
An overview of RDP Classifier, no longer online, but can be downloaded to your own computer.
A brief biography of JBS Haldane, and the story of his wonderful quote about beetles.
A nice overview of microbiology and social equity, from the ASM website.
Dr. Susan Ishaq’s working group of microbiology and social equity.
A great short video about Dr. Jack Gilbert’s interests and philosophy.
Dr. Jack Gilbert’s profile at UC San Diego, and his faculty website at Scripps Institution of Oceanography.
Dr. Jack Gilbert’s laboratory website.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #13: (Magnetically) attractive bacteria with Arash Komeili Oct 27, 2023

Today Dr. Arash Komeili, professor of plant and microbial biology at UC Berkeley, joins the #QualityQuorum to discuss compartmentalization in bacteria, and the amazing world of living magnets—the magnetotactic bacteria!

Host: Mark O. Martin

Guest: Arash Komeili

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Links for this episode

“Hooked by Bex”’s Etsy page.
An introduction to Paenibacillus.
More wonderful information on this fascinating bacterium.
Another remarkable article on colony pattern formation by this microbe.
An interesting essay about how Paenibacillus can move other organisms around, from the wonderful Small Things Considered blog.
Muriwai Beach in New Zealand.
Magnetic sand in New Zealand article.
A lovely introductory video about magnetotactic bacteria.
A video “dance” of the magnetotactic bacteria.
An introduction to magnetotactic bacteria.
Techniques to isolate/enrich for magnetotactic bacteria of your own.
A wonderful article on analyzing magnetotactic microbes from the Komeili lab.
Dr. Komeili’s faculty website.
Dr. Komeili’s laboratory website.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #12: Shedding light on symbiosis with Ruth Isenberg Oct 20, 2023

Today Dr. Ruth Isenberg, postdoctoral scholar (and former #DocMartian!) in the Willett Lab at the University of Minnesota, will tell us about her first generation path in science, the squid-Vibrio symbiosis work she did for her PhD, and her current career path.

Host: Mark O. Martin

Guest: Ruth Isenberg

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Links for this episode

The Sikhote-Alin meteorite fall.
An article on Kenyan Sand Boas.
An article on African Fire Skinks.
A video reminder about ice nucleation bacteria.
An article relating snowflakes to ice nucleation bacteria
A reminder of the nature of bacterial colonies.
The laboratory website of Dr. Kat Milligan-McClellan.
The laboratory website of Dr. Mark Mandel.
The laboratory website of Dr. Julia Willett.
A great place to begin thinking about the squid-Vibrio symbiosis, as well as the microbiome in general.
An excellent review article on the squid-Vibrio symbiosis.
A fun and accessible video from the famed science journalist Ed Yong about the squid-Vibrio symbiosis.
An article written by Ruth about her work on this symbiosis
Ruth’s excellent claymation video made for my microbiology class about quorum sensing and the squid-Vibrio symbiosis. Student creativity matters!
Another #Micronaut’s claymation video about Type VI secretory systems. Student creativity matters!

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #11: Viruses from hell with Ken Stedman Oct 13, 2023

Today Dr. Ken Stedman, Professor of Biology at Portland State University, tells us about the strange and wonderful viruses of heat loving extremophilic archaea—truly viruses from Hell!

Host: Mark O. Martin

Guest: Ken Stedman

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Links for this episode

A popular article about Markus Martin’s work as a fossil expert extraordinaire.
Markus Martin’s website.
One of Markus Martin’s academic articles on trilobites.
An interesting article on the complexity of colony morphology by Bacillus subtilis.
An article about Serratia, prodigiosin, and temperature.
An article I wrote about educational aspects of the work of the late great Carl Woese.
An introduction to the diverse and fascinating archaea.
An introduction to the viruses of archaea.
Ken Stedman’s fascinating laboratory website.
Ken Stedman’s faculty website.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #10: Bacterial fight club Oct 06, 2023

Today Dr. David Baltrus, Associate Professor of Plant Sciences at the University of Arizona, talks with us about how his laboratory studies bacteria that battle one another; the first rule of this fight club is that EVERYONE talks about Microbial Fight Club.

Host: Mark O. Martin

Guest: David Baltrus

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Links for this episode

Here is a wonderful and easy to read essay about bacterial predators, including Bdellovibrio, from Scientific American.
“2001: A Space Odyssey” remains an important motion picture.
The animated movie “The Iron Giant” is entertaining and has important messages.
Kaitlin Kariko, Drew Weissman, and the 2023 Nobel Prize in Physiology and Medicine.
Jo Handelsman’s wonderful “Tiny Earth” program, helping students to search for new antibiotic producing bacteria.
Elio Schaechter’s absolutely essential guide/view of the changing microbial landscape in terms of organizing our knowledge.
A nice introductory review of tailocins.
A more exhaustive review of talocins.
A really interesting article on this topic—and how tailocins might be used in agriculture— from Dr. Baltrus’ laboratory.
Dr. Baltrus’ laboratory website can be found here.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #9: Colorful microbes, citizen science, and tools for all Sep 29, 2023

Today Sebastian Cocioba, a citizen scientist with myriad interests, talks with us about his path in science, some of the tools he has made for others, and how he views science and scientists.

Host: Mark O. Martin

Guest: Sebastian Cocioba

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Links for this episode

The article on Carl Woese that I wrote can be found here.
An article on the felt sculpture of Carl Woese is here.
The artist who created that sculpture, Amy Wright, has a website here.
The American Society for Microbiology’s moving and informative video about Carl Woese is here.
A heartwarming snippet from “Ted Lasso” regarding the Walt Whitman quote is here.
Here is a great interview with Sebastian Cocioba.
Sebastian Cocioba’s website is here.
Sebastian Cocioba’s online research notebook is here.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #8: Who goes there? Going deep in the Pine Barrens with Lauren Seyler Sep 22, 2023

Microbes are everywhere and do remarkable things—-like breathing metal! Lauren Seyler joins us today to discuss the microbial mysteries of New Jersey’s Pine Barrens.

Host: Mark O. Martin

Guest: Lauren Seyler

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Links for this episode

A beautiful essay on tardigrades can be found here.
Weird and wonderful (mythical?) cryptids around the US described here. Hallowe’en fun!
Frivolous Forest’s site on Etsy is here.
A lovely overview of the Pine Barrens is here.
Some of the unusual legends of the Barrens can be found here.
An article about “bog iron” is here.
An overview of iron-related microbes is here.
An abstract of a research talk about bog iron related microbiology from Dr. Seyler’s group can be found here.
Dr. Seyler’s departmental site is here.
Dr. Seyler’s fascinating lab website is here

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #7: Microbiology from the refrigerator with Elinne Becket Sep 15, 2023

We exist in a sea of microbes, it is true. We only need to look. And Dr. Elinne Becket of California State University San Marcos, joins Mark to describe some of the work she and her undergraduate colleagues are doing. And a popular hashtag on social media: #BlueSoup. Welcome to our quality quorum, Elinne!

Host: Mark O. Martin

Guest: Elinne Becket

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Links for this episode

An essay on gooseneck flasks, Louis Pasteur, and spontaneous generation can be found here.
Lizah van der Aart creates wonderful microbiologically oriented pins here.
Caulobacter is a fascinating organism, as you can see here.
Here is a short video of the #LuxArt made by my #Bio350 #Micronauts this fall.
Maggie Middleton creates fabulous science art here.
A wonderful description of Dr. Becket’s #BlueSoup story.
Another telling of the #BlueSoup tale!
Dr. Becket’s wonderful laboratory website can be found here.
Dr. Becket’s thread on Twitter/X describing the #BlueSoup excitement as it happened is here.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #6: What's the buzz on honeybee microbes? With Irene Newton Sep 07, 2023

It is true that microbes are everywhere, and have impacts and applications that are often unexpected. Today, a true microbial force of nature visits Matters Microbial: Dr. Irene Newton of the Biology Department of the University of Indiana. Irene will tell us about some of her laboratory group’s recent research on how microbes interact with honeybees!

Host: Mark O. Martin

Guest: Irene Newton

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Links for this episode

A review of manganese oxidizing bacteria can be found here.
An essay on ice nucleating bacteria can be found here.
A review of bacterial siderophores can be found here.
A press release on the work that Dr. Newton and her research group does can be found here.
Here is another such press release.
A sample publication from Dr. Newton’s laboratory is here.
Dr. Newton’s faculty website is here
Dr. Newton’s laboratory website can be found here.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #5: Mothers, Microbes, and Dung Beetles Sep 01, 2023

It’s interesting to think about the microbes in and on us—some of which are vital to our well being—and how we came to possess them. Mark introduces Dr. Anne Estes of Towson University, who will discuss this very topic as it applies to dung beetles.

Host: Mark O. Martin

Guest: Anne Estes

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Links for this episode

Microbial fossils—stromatolites—are fascinating. A description of Gunflint stromatolites can be found here.
Rachael Webster (wonderful artist) can be found here.
Jane Hartman’s wonderful art is found here.
Dr. Jack Gilbert’s book, “Dirt is Good” is described here.
A video about the life of dung beetles is here.
Dr. Estes’ faculty website is here.
Dr. Estes blog can be found here.
Here is an article that Dr. Estes wrote: “Brood Ball-Mediated Transmission of Microbiome Members in the Dung Beetle, Onthophagus taurus.”

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #4: Extreme Microbial Closeups: Cryo-EM and Fine Structure of Microbes with Ariane Briegel Aug 25, 2023

Everyone thinks microbes are very small, and most of them are. But how to see them? The microscope opened a whole new world to the observer, starting with the Dutch microbiologist Antonie van Leeuvenhoek. But photographs and peering through lenses have limitations. Mark introduces his friend and colleague, Ariane Briegel of the Institute of Biology at Leiden University to Matters Microbial. She discusses how her own work can allow us to see microbes at extremely fine detail using a technique called cryo-electron microscopy (cryEM). She will also discuss her path in science.

Host: Mark O. Martin

Guest: Ariane Briegel

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Links for this episode

The Martian meteorite from which my specimen was taken is described here.
Custom enamel pins by Hartiful can be found here.
The website of the great microbiologist and science artist Lizah van der Aart is here.
Here is a video discussing the role played by van Leeuvenhoek in microbial science that is SO worth your time.
Dr. Briegel’s lab website is very interesting.
An explainer about cryoEM can be found here
A really fine talk by Dr. Briegel about her work from ASM Microbe a few years ago.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #3: How much of you is microbial? With Seth Bordenstein Aug 18, 2023

Who are you? Human or a group of microbes? Mark discusses this with this with Dr. Seth Bordenstein of Penn State. Seth teaches Mark about a new word, holobiont, and the most successful pandemic in history (of invertebrates) that may help in the fight against malaria, Wolbachia! Finally, Seth discusses his team outreach efforts to teach critical thinking and STEM in students with Discover the Microbes Within.

Host: Mark O. Martin

Guest: Seth Bordenstein

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Links for this episode

Maggie Middleton’s (the “Vexed Muddler”) art website.
Seth Bordenstein’s lab website.
Discover the Microbes Within website.
A useful review of the holobiont concept from the Proceedings of the National Academy of Sciences.
A recent and philosophical review of the holobiont concept from Frontiers in Psychology.
Another review of the holobiont concept from the American Society for Microbiology.
Wood rats, creosote, and the microbiome via Kevin Kohl in Frontiers in Microbiology.
Evidence that the microbiome can impact drug effectiveness in Gut.
A review on Wolbachia and the effect it has on hosts in Nature Reviews in Microbiology.
An article describing how Wolbachia can be used to fight viral diseases in Frontiers in Immunology.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #2: Shock and awe microbiology and a chat with Mya Breitbart Aug 11, 2023

Mark discusses some “shock and awe” concepts about the microbial world that he introduces to his microbiology students, and asks three important questions about microbiology and microbiologists with guest Dr. Mya Breitbart of the University of South Florida.

Host: Mark O. Martin

Guest: Mya Breitbart

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Links for this episode

MicrobeTV Discord Server
Ice nucleation information
A video of ice nucleation
A funny video by my students
Deinococcus radiodurans
Pink pigmented methylotrophs
Some wonderful #LuxArt sessions I have done: one, two, three, four
Dr. Breitbart’s faculty website
Dr. Breitbart’s laboratory website
Dr. Breitbart’s visit to This Week in Virology

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #1: A microbiological introduction and a chat with Vincent Racaniello Aug 07, 2023

In the first episode of Matters Microbial, Mark introduces himself and his history, talks a bit about his goals for this podcast, then asks three important questions about microbiology and microbiologists with his first guest, Vincent Racaniello.

Host: Mark O. Martin

Guest: Vincent Racaniello

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Links for this episode

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com