Matters Microbial

Matters Microbial #96: Molecular Microbiology in High Schools June 19, 2025 Today, Bob Kuhn, biotechnology teacher at the Fulton County Schools Innovation Academy STEM high school in Alpharetta, Georgia joins the #QualityQuorum to discuss his strategies for teaching molecular microbiology skills and concepts to high school students — and why that matters. Host: Mark O. Martin Guest: Bob Kuhn Subscribe: Apple Podcasts, Spotify Become a patron of Matters Microbial! Links for this episode An article on Mr. Kuhn's original microbiological interest:  salt marsh foraminifera. Another interest:  a video of the beautiful organism Volvox. An overview of the fantastic world of protists. A classroom CURE that Mr. Kuhn uses:  the Tiny Earth program. A classroom CURE that Mr. Kuhn uses:  the SEAPHAGES program. A classroom CURE that Mr. Kuhn uses:  the Evolving Stem program. A classroom CURE that Mr. Kuhn uses:  the Discover the Microbes Within program. Mr. Kuhn's classroom received help from the University of Georgia Microscopy Center. A video of the Wolbachia Project with which Mr. Kuhn has collaborated for years. An overview of wonderful and various isopods, including the “roly polies” used in some Wolbachia work. The Journal of Emerging Investigators, in which some of Mr. Kuhn's high school students have published. The LTEE program that studies evolution in E. coli.   The Experiment.com program that supported some of Mr. Kuhn's students. The very inspirational MEGAplate video that demonstrates how quickly antibiotic resistance can occur. Innovation Academy STEM program in Georgia, where Mr. Kuhn works with high school students. Intro music is by Reber Clark Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #95: Bacteria and Aphids — A Symbiotic Story June 12, 2025 Today, Dr. Tory Hendry, Associate Professor of Microbiology at Cornell University, joins the #QualityQuorum to tell us about the relationship between plant munching aphids and fluorescent Pseudomonas . . . and why we should care. Host: Mark O. Martin Guests: Tory Hendry Subscribe: Apple Podcasts, Spotify Become a patron of Matters Microbial! Links for this episode An overview of siderophores in microorganisms. An essay about aphid life cycle and characteristics. An article describing parthenogenesis in aphids. An essay describing aphids and color vision. The agricultural costs of aphids as pests. An article describing aphids and one type of bacterial symbiont. An overview of microbes of the phyllosphere. An overview of quorum sensing. An overview of pyoverdin, a fluorescent siderophore.  An old essay I wrote for the Small Things Considered blog about semiochemicals, bacterial, and insect predation. A nice description of the work Dr. Hendry talked about during today's podcast.  The actual article by Dr. Hendry and collaborators. A preprint by Dr. Hendry's research group, following up on the above research.  Dr. Hendry's faculty website. Dr. Hendry's research group website (with SO MANY cool projects to think about, including the topic discussed today). Intro music is by Reber Clark Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #94: One Health and Microbiomes Everywhere June 5, 2025 Today, Dr. Seth Bordenstein and Dr. Nichole Ginnan of Pennsylvania State University join the #QualityQuorum to tell us about their new publication linking One Health to the myriad microbiomes that exist all around us through the lens of the holobiome—and an opportunity to see the world in a different fashion. Host: Mark O. Martin Guests: Seth Bordenstein and Nichole Ginnan Subscribe: Apple Podcasts, Spotify Become a patron of Matters Microbial! Links for this episode Michele Banks microbially themed art can found at her Etsy site.  Highly recommended! The paper under discussion today, with Dr. Ginnan as first author.  You will see that coauthors include Dr. Bordenstein, and two previous visitors to the #MattersMicrobial podcast!  Thank you Erika and Francisco. Dr. Bordenstein's first podcast with #MattersMicrobial for those who missed it. A review of the One Health concept. The One Health Microbiome Center at Penn State. A very clear overview of the holobiont concept and biology, authored by Dr. Bordenstein and colleagues. Another longer review on this topic. The faculty website for Dr. Ginnan. The faculty website for Dr. Bordenstein. The research website for Dr. Ginnan. The research website for Dr. Bordenstein. Intro music is by Reber Clark Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #93: Preventing Antibiotic Resistance May 29, 2025 Today's episode was an in-person podcast at the University of Texas Austin!  Dr. Despoina Mavridou, Assistant Professor of Molecular Biosciences, joins the #QualityQuorum to discuss how her research group improves antibiotic effectiveness by impeding protein folding, and why this matters in the fight against antimicrobial resistance. Host: Mark O. Martin Guest: Despoina Mavridou Subscribe: Apple Podcasts, Spotify Become a patron of Matters Microbial! Links for this episode Here is a link to a wonderful video of the #LuxArt by UT-Austin students during my visit. Please give it watch and enjoy the creativity and positive #MicrobialPR. An effective TED talk by science journalist Maryn McKenna describing the threat of AMR in an accessible fashion. A CDC report on the growing threat of AMR. A review article about antibiotics. An overview of how bacteria become resistant to antibiotics.  A very recent review of the cell wall of bacteria—often the target of antibiotics. A video overview of beta-lactam antibiotics and resistance mechanisms. An overview of how protein folding is related to activity of proteins…including AMR gene products. A wonderful article by Dr. Mavridou and coworkers, describing how altering protein folding in bacteria can make them more vulnerable to antibiotics. A less technical version of the above article; well worth your reading. Dr. Mavridou's faculty website. Dr. Mavridou's research group website, which is most interesting. Intro music is by Reber Clark Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #92: Microbial Metabolism in Extreme Places May 22, 2025 Today, Dr. Valerie DeAnda Torres, Assistant Professor of Microbiology and Cell Science at the University of Florida (and National Geographic Explorer), joins the #QualityQuorum to tell us about the research her team does, studying the evolution of metabolic pathways in extreme environments . . . and why these are important to geochemical cycling. Host: Mark O. Martin Guest: Valerie DeAnda Torres Subscribe: Apple Podcasts, Spotify Become a patron of Matters Microbial! Links for this episode The Etsy vendor making the beautiful microbial pins I have mentioned.  A link to Sebastian Cocobia's site where the beautiful E. coli strains I referenced can be obtained.  The beauty and mystery of Paenibacillus colonies. A video showing a colony of Myxococcus consuming a colony of E. coli. A fun video of tardigrades singing “Happy birthday” by a former undergraduate student of mine, Dr. Jake Shaffer. The National Geographic Explorer program, which includes Dr. DeAnda Torres.  The deep sea submersible Alvin, in which Dr. DeAnda Torres has dived!  An overview of methanogenesis, one of the pathways that Dr. DeAnda Torres' research group studies. A review of biogeochemical cycles in the deep ocean. The work of my former undergraduate research student, Dr. Paula Welander, on membrane biosignatures in ancient rocks. A recent review of the Asgard archaea, that may be our ancient ancestors. Some recent work by Dr. DeAnda Torres and collaborators on the Asgard archaea. One of the research cruises in which Dr. DeAnda Torres participated. During one cruise that included an Alvin dive to a hydrothermal vent, Dr. DeAnda Torres and scientists working with her described their work in this livestream partially in Spanish. Dr. DeAnda Torres will be part of some upcoming collaborative research cruises, seen here. Here is an article and video describing some of the collaborative work Dr. DeAnda Torres carries out, studying microbial breakdown of PFAS chemicals in marine sediment. A link to the faculty website of Dr. DeAnda Torres. A link to the research website of the DeAnda Torres group. Intro music is by Reber Clark Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #91: You Are What Your Genes Feed Your Microbiome May 16, 2025 Today, Dr. Emily Davenport, Assistant Professor in the Department of Biology and Huck Institutes of the Life Sciences at Penn State University, joins the #QualityQuorum to tell us about the research her team does, studying how our own genes impact our microbiomes.   Host: Mark O. Martin Guest: Emily Davenport Subscribe: Apple Podcasts, Spotify Become a patron of Matters Microbial! Links for this episode A description of GWAS (“Genome Wide Association Study”).  Here is an introductory video about the concept. An explainer on organoids. An essay about the diversity of the host microbiome (i.e. is there a “healthy” microbiome?). An article of the work of Dr. Sarkis Mazamian on how individual host genes and bacterial genes can impact the microbiome. A nice write up for Dr. Mazamian's work showing how host genes and bacterial genes can work together…or not. An oldish video of how the infant microbiome develops over time by Dr. Rob Knight's research group. An article on the same topic from Dr. Ruth Ley. An essay on the mucosal microbiota, rather than the fecal microbiome. An interesting member of the human microbiome, Akkermansia that might be related to obesity. Another interesting member of the human microbiome, Bifidobacterium, which appears to be associated with host lactose metabolism.  Yes, there is a Giant Microbes plush toy. An overview of the impact of host genetics on the microbiome by Dr. Davenport.  A definition of heritability. An overview of the Hutterites and how their study has advanced genetics. An explainer of the power of twin studies in genetics. A fascinating article about ancient dental plaque microbiome by Dr. Davenport and others. Dr. Davenport's faculty website. Dr. Davenport's research group website. Intro music is by Reber Clark Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #90: Using Soil Microbiomes in Sustainable Agriculture May 8, 2025 Today, Dr. Francisco Dini Andreote, Assistant Professor of Phytobiomes at Penn State, joins the #QualityQuorum to tell us about the microbiome of plants and the soil, and how understanding that relationship can improve agriculture. Host: Mark O. Martin Guest: Francisco Dini Andreote Subscribe: Apple Podcasts, Spotify Become a patron of Matters Microbial! Links for this episode An overview of the Type 6 Secretory System of bacteria—almost like a microbial switchblade knife. A wonderful video of the T6SS made by a student in my own microbiology course some time ago. A video introduction to the Rhizobium-legume symbiosis and why you should care about it (by my PhD advisor from long ago, Dr. Sharon Long). A more comprehensive review article on the Rhizobium-legume symbiosis.  The chemical signal of geosmin, and how it might be used by other organisms. Ecological succession in the development of sauerkraut. A must read essay by Carl Zimmer likening the human body to a number of ecological niches. The developing field of agroecology.  A reminder about the “One Health” concept. Mycorrhizae and plant nutrition. Chemical communication within the soil. A fun remembrance of Norman Borlaug, who urged us to “listen” to plants. An overview of the root microbiome. The “superorganism” concept versus the “holobiome” concept.. Striga, a parasite of crop plants. Chemical communication and Striga.  An interesting and relevant publication from Dr. Dini Andreote's research group, describing how the root microbiome could help agriculture.  Dr. Dini Andreote's faculty website. Dr. Dini Andreote's very wonderful research team website. Intro music is by Reber Clark Send your questions and comments to mattersmicrobial@gmail.com

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

Matters Microbial #79: How Amoebae Beat the Heat February 20, 2025 Today, Dr. Angela Oliverio, Assistant Professor in the Biology Department at Syracuse University, joins the #QualityQuorum to discuss what her research group has been learning about extremophilic single-celled eukaryotes! Host: Mark O. Martin Guest: Angela Oliverio Subscribe: Apple Podcasts, Spotify Become a patron of Matters Microbial! Links for this episode An overview of protists.   A wondrous video of the types of protists to be found seemingly everywhere. A video about amoebae and how YOU can find them.   A video about the testate amoebae mentioned in this podcast. An essay about the testate amoebae. A very old article on temperature limits to eukaryotic life. A more modern article on this topic. An article from Dr. Oliverio's group on the temperature limits to eukaryotic life. The Mullin laboratory at UCSF does remarkable visualization. Genomics and the Lawrence Livermore Laboratory. How mycoplasma move, with remarkable videos. A member of Dr. Oliverio's lab creates beautiful glass art at this Etsy shop. A wonderful local news report on Dr. Oliverio and coworker's research. A nice overview of Dr. Oliverio's research interest in extremophilic protists. An article from Dr. Oliverio's group explaining why we should all care about extremophilic eukaryotes. Dr. Oliverio's research website (and SO worth your time) Dr. Oliverio's faculty website. Intro music is by Reber Clark Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #78: An EXTREME Close Up of the Squid-Vibrio Symbiosis February 13, 2025 Today, Dr Ariane Briegel, Professor and head of the Integrative Structural Cell Biology research unit at the Institut Pasteur in Paris, France, joins the #QualityQuorum to discuss some of the exciting findings of her research group studying how bacteria and the ever-popular Hawaiian bobtail squid work together at a  molecular level—using cutting-edge cryo-electron  tomography! Host: Mark O. Martin Guest: Ariane Briegel Subscribe: Apple Podcasts, Spotify Become a patron of Matters Microbial! Links for this episode The (somewhat venerable) “The Eighth Day of Creation” discussed in this episode. A lovely article about the much missed Dr. Esther Lederberg.  Here is another I much enjoyed.  A website devoted to Dr. Esther Lederberg. A fun video reminder of the symbiosis between Vibrio fischeri and Euprymna scolopes.   A review of cryo-electron tomography as applied to the study of bacterial structures. A book coauthored by Dr. Briegel on the use of this technology to study cell-microbe interactions. A video on the topic of cryo-electron tomography. Another video by Dr. Briegel on this topic.   An earlier episode of #MattersMicrobial with Dr. Briegel. An article by the Moore Foundation that supports the work of Dr. Briegel. A article describing how cryo-EM can be applied to whole organisms, like roundworms.   Research websites for collaborators on this project, Dr. Edward Ruby and Dr. Margaret McFall-Ngai. Dr. Briegel's laboratory website. Dr. Briegel's academic website. Intro music is by Reber Clark Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #77: It's a Germ-Eat-Germ World! February 6, 2025 Today, Dr Laura Williams, Director of Undergraduate Research at Georgia Institute of Technology, joins the #QualityQuorum to discuss some of the exciting work she did as an associate professor at Providence College with undergraduate students studying predatory bacteria and why we should care about this fascinating topic! Host: Mark O. Martin Guest: Laura Williams Subscribe: Apple Podcasts, Spotify Become a patron of Matters Microbial! Links for this episode A quite ancient review article describing the different classes of predatory bacteria by yours truly. A very important article on this topic by the late Dr. Lynn Margulis and colleagues. An article about my very inspirational first microbiology professor at UCLA, Syd Rittenberg, who did early work on Bdellovibrio. Several more up to date review articles on Bdellovibrio. The website of Dr. Liz Sockett (where both yours truly and Dr. Williams received some generous training). A quite interesting article by Dr. Sockett on Bdellovibrio. An article suggesting that predatory bacteria could be used as “living antibiotics.” An article describing the BALOs concept. The article described by Dr. Williams. Dr. Williams laboratory group website. Dr. Williams current faculty/administrator page. Intro music is by Reber Clark Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #76:  Marvelous Multicellular Magnetotactic Microbes! January 29, 2025 Today, Dr. George Schaible, Postdoctoral Scholar at the University of California, Santa Barbara, joins the #QualityQuorum to discuss the exciting work he did during his PhD to unravel a fascinating topic:  multicellular magnetotactic microbes!   Host: Mark O. Martin Guest: George Schaible Subscribe: Apple Podcasts, Spotify Become a patron of Matters Microbial! Links for this episode What is a postdoctoral scholar in microbiology?  A previous #MattersMicrobial podcast about giant bacteria from Dr. Esther Angert.   A previous #MattersMicrobial podcast about magnetotactic bacteria from Dr. Arash Komeili. A previous #MattersMicrobial podcast about multicellularity in microbes from Dr Will Ratcliff.   The transformative Microbial Diversity Course at the Marine Biological Labs at Woods Hole, Massachusetts. An article describing the value of the Microbial Diversity Course.  I wrote this blog post on Chlorochromatium aggregatum consortium for Small Things Considered many years ago.   The “pink berry” consortium at Woods Hole. A research paper on genetic interactions within the pink berry consortium, coauthored by a former undergraduate researcher of mine, Dr. Danielle Campbell.  Yes, I am very proud. A strategy to easily enrich for magnetotactic bacteria from nature. Here is a video that informs and amuses.   An early report of multicellular magnetotactic microbes. The research article under discussion in today's podcast. A link to Dr. Roland Hatzenpichler's laboratory website (Dr. Hatzenpichler was the originator of this research, all the way back to his own attending the Microbial Diversity Course.). The deeply strange genome(s) of Achromatium. An introduction to nanoSIMS technology. An introduction to stable isotope probing. The laboratory website of Dr. Jean-Marie Volland, where Dr. Schaible works at UC Santa Barbara Intro music is by Reber Clark Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #75: Do Gut Microbes Watch their Carbs?   January 22, 2025 Today, Dr. Darrell Cockburn, Associate Professor of Food Science at Penn State, joins the #QualityQuorum to discuss the work his research group has done exploring how starches and other polysaccharides are used by the gut microbiome.  Host: Mark O. Martin Guest: Darrell Cockburn Subscribe: Apple Podcasts, Spotify Become a patron of Matters Microbial! Links for this episode An overview of dietary fiber in the diet. A primer on the structure of starch and cellulose. An overview on starch granules. The concept of food gelatinazation. An overview of “resistant” starch. How Febreze works! The concept of the glycemic index of foods. An article about resistant starch and colon microbiota.  Another article on this topic. A primer on carbohydrate binding modules. An article describing the role of short chain fatty acids in digestion. An article suggesting that there is no perfect microbiome. An interesting article from Dr. Cockburns research group showing that microbes can work together to digest resistant starch. Dr. Cockburn's academic website. Intro music is by Reber Clark Send your questions and comments to mattersmicrobial@gmail.com

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

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

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 Subscribe: Apple Podcasts, Spotify Become a patron of Matters Microbial! 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 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 Subscribe: Apple Podcasts, Spotify Become a patron of Matters Microbial! 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 Synechococcus Figure 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 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 Subscribe: Apple Podcasts, Spotify Become a patron of Matters Microbial! 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 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 Subscribe: Apple Podcasts, Spotify Become a patron of Matters Microbial! 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 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 Subscribe: Apple Podcasts, Spotify Become a patron of Matters Microbial! 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 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 Subscribe: Apple Podcasts, Spotify Become a patron of Matters Microbial! 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

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 Subscribe: Apple Podcasts, Spotify Become a patron of Matters Microbial! 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 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 Download MM#57 (39 MB mp3, 65 min) Subscribe: Apple Podcasts, Spotify Become a patron of Matters Microbial! 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 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 Subscribe: Apple Podcasts, Spotify Become a patron of Matters Microbial! 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

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

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

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

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

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

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

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

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

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

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