Matters Microbial

Latest Episodes:

Matters Microbial #89: Can AI Point Us to New Antibiotics May 01, 2025

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Matters Microbial #89: Can AI Point Us to New Antibiotics May 1, 2025

Today, Dr. Amir Mitchell, Associate Professor of Systems Biology at the University of Massachusetts Medical School, joins the #QualityQuorum to discuss using artificial intelligence to develop new and effective antibiotics in our endless battle against drug-resistant microbes.

Host: Mark O. Martin

Guest: Amir MItchell

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Links for this episode

An article exploring the impact of the microbiome on drug effectiveness.
A blog post discussing the relationship between the gut microbiome and creosote metabolism in wood rats.
An essay about the threat of antibiotic resistance.
A more scholarly article on this topic.
A CDC report of the rise of antibiotic resistance.
A very moving TED talk on this topic.
An overview of antibiotic resistance mechanisms.
A video from Dr. Michael Baym's laboratory demonstrating how rapidly antibiotic resistance can occur.
An essay discussing the use of artificial intelligence in the search for new antibiotics.
An article from Dr. Mitchell's research group discussing his approach to identity new antimicrobial compounds.
Dr. Mitchell's faculty website.
Dr. Mitchell's very interesting research team website.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #88: Microbial Interactions in Cystic Fibrosis Apr 24, 2025

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Matters Microbial #88: Microbial Interactions in Cystic Fibrosis April 24, 2025

Today, Dr. Reed Stubbendieck, Assistant Professor of Microbiology & Molecular Genetics at Oklahoma State University joins the #QualityQuorum to discuss how microbes and the host communicate with one another in the cystic fibrosis lung.

Host: Mark O. Martin

Guest: Reed Stubbendieck

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Links for this episode

An overview of cystic fibrosis as a disease with a genetic link.
A review of the microbiome of the cystic fibrosis lung.
An overview of biofilms.
An interesting role for extracellular DNA itself as a "building block" of biofilms.
An overview of polymicrobial communities.
Life in mucus—an interesting essay.
An overview of Pseudomonas aeruginosa.
Pseudomonas and the siderophore pigment pyoverdin which is not only about iron, but also bacterial conflict and cooperation.
An interesting overview of microbe-microbe interactions, often called "sociomicrobiology," and an introductory article on this topic.
A review of the nasal microbiome.
The organism Rothia, understudied and of interest to Dr. Stubbendieck's research group.
Some work from Dr. Stubbendieck's group describing how Rothia is helpful in inhibiting some disease causing bacteria.
The organism Dolosigranulum pigrum, also understudied and of interest to Dr. Stubbendieck's research group.
More work from Dr. Stubbendieck's group with another possibly probiotic bacterium, Dolosigranulum pigrum, that may protect against disease causing microbes.
Dr. Stubbendieck's faculty website.
Dr. Stubbendieck's very interesting research group website.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #87: Dietary Protein and the Microbiome Apr 17, 2025

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Matters Microbial #87: Dietary Protein and the Microbiome April 17, 2025

Today, Dr. Manuel Kleiner, Associate Professor of Microbiomes and Complex Microbial Communities at North Carolina State University, joins the #QualityQuorum to discuss how diet can influence the microbiome in fascinating ways.

Host: Mark O. Martin

Guest: Manuel Kleiner

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Links for this episode

An overview of "pink pigmented facultative methylotrophs," which can lead to wonderful "leaf prints."
Gnotobiotic versus "germ-free" animals.
A solid review of the gut microbiome and the relationship to health.
An article describing how proteins are digested by the microbiota.
A description of glycan degrading enzymes and the gut microbiome.
An overview of mucin.
Description of metaproteomics by Dr. Kleiner.
Description of metagenomics.
Gut microbiota and dysbiosis.
An overview of inflammatory bowel disease.
An overview of Bacteroides thetaiotaomicron.
An overview of Akkermansia muciniphila.
The possibility of microbes "farming" us for mucus!
The wide ranging and deeply fascinating website for Dr. Kleiner's research group.
Dr. Kleiner's faculty website.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #86: Intraterrestrials — the Strangest Life on, and in, the Earth Apr 10, 2025

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Matters Microbial #86: Intraterrestrials — the Strangest Life on, and in, the Earth April 10, 2025

Today, Dr. Karen Lloyd, Professor of Earth Science at the University of Southern California, joins the #QualityQuorum to discuss her upcoming book Intraterrestrials (Princeton University Press). Dr. Lloyd will describe the 25 year journey she and her coworkers have had exploring microbial life deep underground, and even less likely places.

Host: Mark O. Martin

Guest: Karen Lloyd

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Links for this episode

The upcoming book, Intraterrestrials, by Dr. Lloyd.
Definition of the term "intraterrestrial."
An interesting review article on intraterrestrial microbes.
An video overview of extremophiles.
An overview of the new field of geomicrobiology.
A definition of "SLiME"s (subsurface lithoautotrophic microbial ecosystem).
An article on microbial communities found deep underground.
An article on "just underground" microbial communities that was just published.
Remembering Dr. Katrina Edwards.
Microbial communities in New Zealand hot springs.
Radiolytic microbial communities.
Photosynthesis by cyanobacteria via deep infrared light at hydrothermal vents (without sunlight).
Microbes living under extreme acidic conditions: the famed "snottites."
Microbes living under extreme alkaline conditions: NPL-UPL2.
How slowly can microbes divide?
A fascinating video by Dr. Lloyd.
Introducing Dr. Lloyd in her new position at the University of Southern California (an excellent overview of her work).
Dr. Lloyd's faculty website.
Dr. Lloyd's research group website.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #85: The Microbiomes of Hawai'ian Seascapes Apr 03, 2025

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Matters Microbial #85: The Microbiomes of Hawai'ian Seascapes April 3, 2025

Today, Dr. Rosie 'Anolani Alegado of the University of Hawai'i at Mānoa joins the #QualityQuorum to discuss how weather, climate, and human intervention impact the microbiota to be found in human related seascapes around Hawai'i.

Host: Mark O. Martin

Guest: Rosie 'Anolani Alegado

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Links for this episode

An overview of how Hawai'i was settled from Polynesia.
An essay describing indigenous Hawai'ian culture and its collaborative relationship to the land and sea.
A must read book "Coral Reefs in a Microbial Sea," by the late Merry Youle, Forest Rohwer, and Derek Vosten.
Here are several links related to the work of Dr. Isabella Abbott, including this one from Pacific Science. Again, well worth your reading.
An overview of the field of ethnobotany, championed by Dr. Abbott.
Dr. Alegado's previous research was with the fascinating choanoflagellates, which can tell us about the evolution of complex life. Here is a video about these ancient relatives of us all. Here is a article from Dr. Alegado describing a bacterial role in the development of this fascinating organism.
An overview of the "One Health" concept linking human interactions, animals, plants, the land, and the ocean.
A focus of Dr. Alegado's group research involving the indigenous Hawai'ian fishponds.
An overview of community restoration of these ancient structures.
The role of taro in ethnobotany.
A fine description of indigenous Hawai'ian mariculture.
The concept of dysbiosis.
Tropical storm Wali, which impacted the Hawai'ian Islands.
An overview of alpha diversity and beta diversity in microbiome studies.
A fine book about Dr. Barbara McClintock, "A Feeling for the Organism."
Here is a wonderful video in which Dr. Alegado describes the work of her research group and her interests in the fishponds of Hawai'i.
Dr. Alegado's faculty website.
Dr. Alegado's very interesting research group website.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #84: Detecting Pathogens — and Worse — in Wastewater Mar 27, 2025

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Matters Microbial #84: Detecting Pathogens — and Worse — in Wastewater March 27, 2025

Today, Dr. Rachel Poretsky, Associate Professor of Biological Sciences at the University of Illinois Chicago joins the #QualityQuorum to discuss how examining wastewater (and related water) can give insights into the presence of pathogen antimicrobial resistance genes and even microbial ecology.

Host: Mark O. Martin

Guest: Rachel Poretsky

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Links for this episode

A link to demonstrate the wonders of the Marine Biological Laboratories' Microbial Diversity course, which I know for a fact is life changing.
Recommended by David Ranada, an article about water bottles and microbes.
An essay about the Chicago River and cholera, which led to the necessity of effective waste water treatment.
An overview of the complexities of waste water treatment. Here is a video on that topic.
An essay by Carl Zimmer about the microbial ecology of lakes…and human beings.
How "recreational water quality" is determined.
An article describing the microbiota associated with human biological waste with an amusing name (scroll down).
How qPCR can be used to determine the prevalence of specific microbes.
A recent article from Dr. Poretsky's research group, investigating how antimicrobial resistance genes can move through a hospital waste water system.
A link to the Bacterial-Viral Bioinformatics Resource Center, for which Dr. Poretsky is a Principle Investigator.
The Illinois state wastewater surveillance dashboard. Fascinating!
A Discovery Channel documentary on virus hunting and surveillance that includes Dr. Poretsky.
Dr. Poretsky's faculty webpage.
Dr. Poretsky's webpage for her research group.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #83: Helicobacter — Passing the Acid Test Mar 20, 2025

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Matters Microbial #83: Helicobacter — Passing the Acid Test March 19, 2025

Today, Dr. Karen Ottemann, Professor and Chair of the Department of Microbiology and Environmental Toxicology at the University of California Santa Cruz joins the #QualityQuorum to discuss the fascinating strategies of Helicobacter pylori, which can cause gastric ulcers and even stomach cancer in people.

Host: Mark O. Martin

Guest: Karen Ottemann

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Links for this episode

An overview of Helicobacter pylori and its relationship to gastric ulcers and gastric cancer.
A video on the relationship between Helicobacteri pylori and gastric diseases.
The story of how Helicobacter pylori was finally demonstrated to be responsible for gastric ulcers and gastric cancer.
The prevalence of Helicobacter pylori world wide.
When Helicobacter pylori does not cause disease: a possible theory.
The mechanism by which Helicobacter pylori causes gastric ulcers.
The mechanism by which Helicobacter pylori causes gastric cancer.
An overview of gastric cancer.
An overview of inflammation and cancer.
One of the articles from Dr. Ottemann's research group discussed in this episode: "Bacterial flagella hijack type IV pili proteins to control motility."
Another of the articles from Dr. Ottemann's research group discussed in this episode: "Helicobacter pylori cheV1 mutants recover semisolid agar migration due to loss of a previously uncharacterized Type IV filament membrane alignment complex homolog."
Dr. Ottemann's faculty website.
Dr. Ottemann's research website.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #82: Melanin, Fungi, and Global Warming Mar 13, 2025

Show notes

Matters Microbial #82: Melanin, Fungi, and Global Warming March 13, 2025

Today, the impressive Dr. Arturo Casadevall of Johns Hopkins University returns to the podcast to discuss how fungal disease is a looming threat on our warming planet, and how these organisms can use pigmentation to adapt to human-associated environments . . . and increase their chances of causing disease.

Host: Mark O. Martin

Guest: Arturo Casadevall

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Links for this episode

A video overview of the understudied world of fungi.
A CDC overview of fungal diseases.
A hopeful study: fungi, frogs, and purple bacteria. A less scholarly but highly recommended essay is here.
Dr. Casadevall's earlier visit to #MattersMicrobial.
The story of Alexander Fleming, a stray fungal spore, and penicillin.
The story of fungi and cyclosporins, which help with organ transplantation in humans.
A recent New York Times article on fungal networks.
An article about mass extinctions and "fungal overgrowth."
A review of the structure and function of melanin.
An overview of how melanin can be used to turn various forms of radiation into energy.
A review of high body temperatures versus fungal infections.
One of the articles discussed today, from Dr. Casadevall's group: "Impact of Yeast Pigmentation on Heat Capture and Latitudinal Distribution."
Another article from Dr. Casadevall's group discussed today: "The hypothermic nature of fungi."
A really fascinating preprint from Dr. Casadevall's group discussed today: "Thermal and pigment characterization of environmental fungi in the urban heat island of Baltimore City"
Dr. Casadevall's faculty website.
The research website for Dr. Casadevall's group.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #81: Viruses, Innate Immunity, and Undergraduates Mar 06, 2025

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Matters Microbial #81: Viruses, Innate Immunity, and Undergraduates March 5, 2025

Today, Dr. Brianne Barker, Associate Professor of the Biology Department at Drew University, joins the #QualityQuorum to discuss how her undergraduate research group studies how innate immune mechanisms of cells recognize viral invasion.

Host: Mark O. Martin

Guest: Brianne Barker

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Links for this episode

A video describing the immune system, both innate and adaptive.
More of a focus on mechanisms of innate immunity, the focus for today.
A description of basic immune cells.
An introductory video describing the viral reproductive cycle in general.
A description of PRRs (pattern recognition receptors) and MAMPs (microbially associated molecular patterns)
An overview of interferons and disease.
An introductory video overview of programmed cell death, called apoptosis.
The role that retroviruses play in producing blue eggs in chickens. Here is a very introductory summary.
The role that retroviruses play in placental mammals, including humans.
How do cells recognize invading DNA during viral infection?
A research paper by Dr. Barker's research group.
Dr. Barker on This Week in Virology.
Dr. Barker's faculty website.
Dr. Barker's research group website.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #80: Do Microbes Make the Best Chemists? Feb 27, 2025

Show notes

Matters Microbial #80: Do Microbes Make the Best Chemists? February 27, 2025

Today, Dr. Marc Chevrette, Assistant Professor of Microbiology and Cell Science at the University of Florida, joins the #QualityQuorum to discuss how his research group can study novel metabolites and even interactions via study of microbial genomes! Dr. Chevrette reminds us all that microbes are the best chemists!

Host: Mark O. Martin

Guest: Marc Chevrette

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Links for this episode

An overview of how quickly the field of microbial genomics has advanced.
How secondary metabolites can be important to antibiosis, cell signaling, and even communication.
An overview of genome mining, along with another review.
The program antiSMASH that analyzes genomes for genes involved with secondary metabolites.
A video describing how antiSMASH can be used to search for possible biosynthetic gene clusters.
An essay about Dr. Julian Davies.
An article by Dr. Davies' group suggesting that antibiotics can serve as chemical signals between microbes.
The idea of "parvomics," studying the role of small molecules in how microbes communicate and interact.
A great article from Dr. Chevrette and colleagues about how to look for biosynthetic diversity using genome mining.
An article by Dr. Chevrette and colleagues exploring how groups of microbes can interact in remarkable ways.
Dr. Chevrette's faculty website.
Dr. Chevrette's research website.

Intro music is by Reber Clark

Send your questions and comments to mattersmicrobial@gmail.com

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