Matters Microbial

Matters Microbial #132: What 83,000 Generations of Bacteria Reveal About Evolution June 17, 2026 Today Dr. Jeffrey Barrick, John A. Hannah Distinguished Professor of the Department of Microbiology, Genetics, & Immunology and the Department of Entomology at Michigan State University, joins the quality quorum today to discuss how microbes can be used to study evolution itself. He will also discuss the impressive and ongoing LTEE program, the experiments that originate from it, and what they tell us about evolution. Host: Mark O. Martin Guest: Jeffrey Barrick Subscribe: Apple Podcasts, Spotify Become a patron of Matters Microbial! Links for this episode Here is a link to an article about the late great Abigail Salyers. Here is what I wrote about Dr. Salyers. I learned so much from her. An article about the contributions of Dr. Theodosius Dobzhansky to the study of evolution. The concept of contingency during evolution. An overview of microbial evolution. A link to "Microbes and Evolution," a book discussed during this podcast. A link to "A Primer for Experimental Evolution," a book discussed during this podcast. The concept of Growth Advantage in Stationary Phase (GASP). A video about the MEGA plate experiment by Dr. Michael Baym and colleagues. This is a "must watch." An video about Dr. Richard Lenski, originator of the LTEE. Dr. Lenski's website. The LTEE (long term evolutionary experiment) website. There is so much here to explore. An excellent introduction to the LTEE. An article about the amazing " climbing citrate mountain" innovation during LTEE described in the podcast. A video by Dr. Lenski about LTEE. A video by Dr. Barrick that is worth your time. Dr. Barrick's faculty website at Michigan State University. Dr. Barrick's research laboratory website. Intro music is by Reber Clark Send your questions and comments to mattersmicrobial@gmail.com

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

Matters Microbial #128: C. diff from Nursery to Nursing Home April 20, 2026 Today Dr. Joseph Zackular, Assistant Professor of Pathology and Laboratory Medicine at the Perelman School of Medicine at the University of Pennsylvania, joins the #QualityQuorum to discuss some fascinating microbiology involving the bacterium Clostridiodes difficile (also known as C. diff), which can cause disease in infants, the elderly, and the immunocompromised. Host: Mark O. Martin Guest: Joseph Zackular Subscribe: Apple Podcasts, Spotify Become a patron of Matters Microbial! Links for this episode An essay about siderophores in bacteria. The Giant Microbes "Cdiff" toy. The website of Dr. Patrick Schloss. A link to the #MattersMicrobial podcast with Dr. Schloss. An overview of Clostridioides difficile from a patient / physician perspective. A review article of research involving Clostridioides difficile. An overview on polymicrobial diseases. A wonderful opinion piece by Dr. Arturo Casadevall regarding the term "pathogen." An overview of Enterococcus in the gut microbiome. The technology of imaging mass spectrometry. An article on Stickland fermentation of amino acids among gut bacteria. Work by Dr. Zackular and colleagues discussed in this podcast, describing how FMT can be used as a treatment. Work by Dr. Zackular and colleagues discussed in this podcast, describing how different members of the host microbiome interact, and how that relates to disease. Work by Dr. Zackular and colleagues discussed in this podcast, describing the role of amino acid metabolism to changes in microbiome structure. Work by Dr. Zackular and colleagues discussed in this podcast, describing how Enterococcus can modulate the disease causing characteristics of C. difficile. An interesting paper showing that polymicrobial effects are more common than expected. An article arguing that there is no single "healthy" microbiome. A lovely primer on this topic for most nonmicrobiologists. An overview on fecal microbiome transplants and the treatment of human disease. The website for the Center for Microbial Medicine at the University of Pennsylvania. A great video by Dr. Zackular and colleagues, well worth your time. Dr. Zackular's academic website. Dr. Zackular's laboratory website. Intro music is by Reber Clark Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #126: Squid Eggs Come With Antifungal Frosting March 24, 2026 Today Dr. Spencer Nyholm, Professor in the Department of Molecular and Cell Biology at the University of Connecticut, and Director of the Professional Science Master's Program in Microbial Systems Analysis, joins the Quality Quorum to discuss his research group's work exploring how some squid have harnessed microbes to protect their eggs against pathogens! Host: Mark O. Martin Guest: Spencer Nyholm Subscribe: Apple Podcasts, Spotify Become a patron of Matters Microbial! Links for this episode Here is an overview of coral reef symbioses. The website for the famed Microbial Diversity course at the Marine Biological Laboratory at Woods Hole—a superb and life changing experience for any microbial scientist. An extremely fun video by Ed Yong (featuring Dr. Ned Ruby and Dr. Margaret McFall-Ngai) about the Euprymna scolopes – Vibrio fischeri symbiosis. Prior #MattersMicrobial podcasts related to Euprymna scolopes symbioses from Dr. Ruth Isenberg, Dr. Mark Mandel, and Dr. Margaret McFall-Ngai. The website for Dr. Ruby and Dr. McFall-Ngai which is so very worth your time. An overview of the power of confocal laser microscopy. The Clasi-FISH technique developed by Dr. Jessica Mark Welch (who also was on this podcast, here). The mass spectrometry approach to learning about small bioactive molecules, used by Dr. Marcy Balunas (who also was on this podcast, here). The concept of lightsheet microscopy. Dr. Nyholm discussed his article during the podcast, an overall review of the squid-Vibrio symbiosis. Dr. Nyholm discussed this article during the podcast, from his research team, describing how accessory nidemental gland microbes can protect squid eggs from fungal attack. Dr. Nyholm discussed this article during the podcast, from his research team, describing the development of the accessory nidemental gland and its microbiota. Dr. Nyholm discussed this article during the podcast, describing early work from his research team (including a former undergraduate student of mine!), exploring the microbes associated with the ANG. Concerns about fungal disease and global climate change, described by Dr. Arturo Casadevall (who was on this podcast, here). Searching for BGCs (biosynthetic gene clusters) in hopes of finding antimicrobial compounds. A link to Dr. Nyholm's faculty webpage. A link to Dr. Nyholm's laboratory group webpage. Intro music is by Reber Clark Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #124: How Bacteria Die in the Microbial Marine Forest February 24, 2026 Today Dr. Anne Thompson, Research Assistant Professor in the Department of Biology at Portland State University, joins the #QualityQuorum to discuss the small but necessary microbes in our oceans. They are hugely abundant, use strategies that produce the very oxygen we breathe, and live within an unseen marine jungle! Host: Mark O. Martin Guest: Anne Thompson Download MM124 (37 MB MP3, 62 mins) Subscribe: Apple Podcasts, Spotify Become a patron of Matters Microbial! Links for this episode Here is a wonderful essay about the marine cyanobacterium Prochlorococcus, probably the most abundant photosynthetic organism on Earth. Here is a wonderful presentation about the marine bacterium Pelagibacter, likely the most abundant organism on the planet. Here is a wonderful TED talk by the inspirational Dr. Penny Chisolm of MIT about the wonders of Prochlorococcus. PLEASE watch this wonderful video by a wonderful and inspiring scientist. A description of the Great Oxidation Event, caused by early cyanobacteria, which changed our planet. A lovely and fascinating essay about microbial numbers in the ocean and other ecosystems. A video overview of flow cytometry, which was essential to understanding the very small microbes in the ocean. A Scientific American article about the "Invisible Forest" of marine microbes, by Falkowski. A video overview of the picocyanobacteria, including Synechococcus and previously discussed Prochlorococcus. The essential work of Dr. John Waterbury of the Woods Hole Oceanographic Institute and photosynthetic marine microbes. An overview of the predators of the marine picocyanobacteria by Dr. Thompson and collaborators. The work of Dr. Kelly Sutherland of the University of Oregon, who collaborates with Dr. Thompson. A video describing the wonderfully strange choanoflagellates, which may resemble the first multicellular organisms on our planet, discussed on the podcast. The "mucus nets" of the organisms that Dr. Thompson and collaborators study, which may prey upon picocyanobacteria. A very clear overview of the research interests of Dr. Thompson and her coworkers. A nice video by Dr. Thompson about her research. Dr. Thompson's faculty website at Portland State University. Dr. Thompson's wonderful laboratory website. The website for an upcoming book that Dr. Thompson is preparing on the microbial marine forest and its importance to life on Earth. Intro music is by Reber Clark Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #122: Jumbo Marine Viruses and Nanoscopic Warfare January 26, 2026 Today Dr. Alaina Weinheimer, Simons Foundation Postdoctoral Fellow in Marine Microbial Ecology at the Bigelow Laboratory for Ocean Sciences, joins the #QualityQuorum to discuss new and intriguing marine viruses, including Jumbo Phages! Host: Mark O. Martin Guest: Alaina Weinheimer Subscribe: Apple Podcasts, Spotify Become a patron of Matters Microbial! Links for this episode A video overview of the wonderful world of bacterial viruses, or bacteriophages. A review article describing the roles that bacterial viruses can play in ecology. A description of changes in viral taxonomy, leading to the "realms" concept. An overview of "jumbo phages." Dr. Weinheimer's concept of "wumbology" from the cartoon "Spongebob Squarepants." An article describing host defenses found within bacteriophage genomes. An article by Dr. Weinheimer and colleagues describing lysogeny as a "plastic trait," and the possibility that all bacterial viruses can integrate into host genomes. The Bigelow Laboratory for Ocean Sciences website. The Bigelow Laboratory multimedia site. The webpage for the "Single Cell Genomics Center" at the Bigelow Laboratory. An article by Dr. Weinheimer and colleagues on exploring marine "jumbo phages." Marine "jumbo phages" blogpost for novice micronauts. An article about finding uridine within viral DNA genomes. Dr. Weinheimer's five minute talk about her research—highly recommended. The "Oceans on Tap" Facebook page describing marine biological research at the Bigelow Laboratory.. The Simons Foundation website (which has sadly eliminated the postdoctoral fellowship awarded to Dr. Weinheimer for her work). Dr. Weinheimer's personal website, including background and research interests. Intro music is by Reber Clark Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #120: Bacterial Interactions among Oral Microbes December 29, 2025 For Episode 120, we welcome Dr. Batbileg Bor, Associate Professor at the ADA Forsyth Institute, to the #QualityQuorum. He joins us to discuss some of the oral community's most enigmatic members: microbes that dwell on other microbes and potentially influence our own health. Host: Mark O. Martin Guest: Batbileg Bor Subscribe: Apple Podcasts, Spotify Become a patron of Matters Microbial! Links for this episode Here is a fun video about #LuxArt that Dr. Jennifer Quinn and I made for Harvard University's Microbial Sciences Initiative in 2024. Here is a wonderful essay about Dr. Rita Colwell. Here is a link to her fascinating book about her life. A blog overview of the amazing Deinococcus radiodurans. A fine article about the "artwork" that Paenibacillus creates when it forms colonies. Here is the video that two of my #Bio350 #Micronauts made…a parody of Vanilla Ice's "Ice, Ice, Baby" but about microbiology. Here is a link to the #MattersMicrobial podcast involving the fascinating work of Dr. Jessica Mark Welch on the oral microbiome. A review article on predatory bacteria. An overview of the CPR (Candidate Phyla Radiation), both prominent and mysterious. A recent article by Dr. Bor and colleagues describing the "microbial dark matter" seemingly everwhere…even in the human mouth. An introductory profile on TM7, Saccharibacteria. A solid early review of TM7, by Dr. Bor and colleagues. Dr. Bor and colleagues' early article about TM7, discussed in today's podcast. Dr. Bor and colleagues' article describing interesting interactions between the epibiont and the basibiont, described in today's podcast. Here is a related article. An article by Dr. Bor and colleagues describing the two Type IV pili systems of Saccharibacteria. A fascinating article by Dr. Bor and colleagues describing how TM7 can modulate the responses of animals in different ways, discussed on the podcast. Dr. Bor's LinkedIn profile. Dr. Bor's faculty page at the ADA Forsyth Institute. Dr. Bor's laboratory website with fabulous images to enjoy. Intro music is by Reber Clark Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #118: Biofilms Everywhere! December 15, 2025 Today Dr. Matthew Fields, Director of the Center for Biofilm Engineering at Montana State University, joins the #QualityQuorum to discuss ubiquitous microbial biofilms. These biofilms touch so many aspects of life on Earth, ranging from human health to engineering issues! Host: Mark O. Martin Guest: Matthew Fields Subscribe: Apple Podcasts, Spotify Become a patron of Matters Microbial! Links for this episode The website for the American Society for Microbiology's Conference for Undergraduate Educators. Highly recommended! The must-read story of Angelina Hesse, and the first use of agar to solidify microbiological media. Here is a Kickstarter project involving promoting this important piece of microbiological history. And here is a video made by former podcast guest Dave Westenberg on the Hesse agar story. An engaging video for budding #Micronauts explaining the general concept of quorum sensing in bacteria. A video overview of biofilms on Earth. Perhaps we should call Earth "Planet Biofilm"! Here is an older review of biofilms that is very easy to read and fun to think about. Here is a newer review of the impact that biofilms can have in health, agriculture, industry, and ecology. A video interview with the late "father" of biofilm research, William J. Costerton. The concept that stromatolites are fossilized biofilms. A video describing the biofilm "life cycle." Recent developments in the details of how biofilms form. An article on biofilms and evolution of multicellularity. Previous podcast guest Dr. Vaughn Cooper's "Evolving STEM" outreach project that places biofilms front and center. The challenge of antibiotic resistance and biofilms. The website of the Center for Biofilm Engineering at Montana State University. There is so much to see here, at every level. It is a grand resource for anyone interested in biofilms. The Center for Biofilm Engineers "fact page" on biofilms. Dr. Fields' research page, where you can find information about the kinds of projects discussed today. An engaging video from Dr. Fields institution on biofilms. Dr. Fields' faculty page. Intro music is by Reber Clark Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #116: Microbes in the Concrete Instead of the Abstract November 14, 2025 Today Dr. Julie Maresca, Associate Professor in the Department of Chemistry at the SUNY College of Environmental Science and Forestry joins the #QualityQuorum to discuss how bacteria can interact with a ubiquitous part of modern life: concrete! Host: Mark O. Martin Guest: Julie Maresca Subscribe: Apple Podcasts, Spotify Become a patron of Matters Microbial! Links for this episode Hartiful, the vendor that makes the enamel pins I often show on the podcast. An overview of microbes and the "built environment." An article about how concrete is made. A video on how concrete is made. The concept of "self repairing" concrete. An overview of the microbial limits to life with regard to pH. A description of alkalinophilic bacteria. Biofilms that form on concrete. Difficulties in obtaining DNA from rock. An overview of oligotrophic microbes. The alkali-silica reaction in concrete. Challenges of road salt and concrete. An overview of halophilic microbes. An overview of xerophilic microbes. The concept of SLiME communities. The term aeonophiles. Is "Roman" concrete self-repairing? A company that produces "microbial concrete." An article relevant to today's discussion by Dr. Maresca and colleagues. Dr. Maresca's faculty website. Dr. Maresca's wonderful and artistic research website. Intro music is by Reber Clark Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #114: A Tongue-n-Cheek Look at the Oral Microbiome October 31, 2025 Today Dr. Jessica Mark Welch, Professor at the ADA Forsyth Institute joins the #QualityQuorum to discuss the complex and interactive microbial communities living unseen within our mouths . . . and what those communities can tell us. Host: Mark O. Martin Guest: Jessica Mark Welch Subscribe: Apple Podcasts, Spotify Become a patron of Matters Microbial! Links for this episode Here is a link to the very funny Carisa Hendrix's character "Lucy Darling." I think I made a #Micronaut out of her! A link to the wonderful microbiological art of Dr. Lizah van der Aart. An overview of FISH technology for visualizing DNA and microbes. A reference to R2A medium which helps grow water associated microbes. The anatomy of the human tongue. The infamous and very interesting article describing how microbes are transmitted between partners via kissing. An overview of the oral microbiome. The relationship between oral microbiota and blood pressure. An article by Dr. Mark Welch and colleagues describing a method for visualizing oral microbial communities. An article by Dr. Mark Welch and colleagues about how her techniques can study the kelp microbiome microbiogeography. An article by Dr. Mark Welch and colleagues about the oral microbiome. An article by Dr. Mark Welch and colleagues about the unusual "corncob" microbes to be found on the human tongue. An article by Dr. Jo Handelsman and colleagues describing the THOR soil community, in which even a few members create very diverse responses to the environment. An article by Dr. Mark Welch and colleagues about the role of mucus in the oral microbiome. An overview of the Forsyth Institute and its mission. The Human Oral Microbiome Database website. The website for Dr. Mark Welch. A fun video snippet with Dr. Mark Welch. Intro music is by Reber Clark Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #112: Bacterial Size, Stress, and Antibiotic Resistance October 17, 2025 Today Dr. Petra Levin, the George and Irene Freiberg Professor of Biology at Washington University in St. Louis joins the #QualityQuorum to discuss her work with bacterial cell size, environmental stress on bacteria, and antibiotic resistance. Host: Mark O. Martin Guest: Petra Levin Subscribe: Apple Podcasts, Spotify Become a patron of Matters Microbial! Links for this episode An overview of the periplasm, found in Gram negative bacteria. An overview of beta-lactam antibiotics. The field of quantitative microbiology. An overview of B. subtilis. An overview of E. coli. An overview of Klebsiella. The biography of Barbara McClintock, "A Feeling for the Organism." A video explanation of the lac operon of E. coli. The LTEE program (Long Term Evolution Experiment) founded by Dr. Rich Lenski. The nomenclature of monoderm and diderm bacteria. A video explanation of peptidoglycan in bacteria. Penicillin binding proteins (PBP) and antibiotic resistance. A video about cell division in E. coli. A famous article coauthored by Dr. Elio Schaechter that describes cell growth and cell size in bacteria. A related article by Dr. Levin and colleagues. An overview of ESKAPE bacteria. An article from Dr. Levin's research group describing the relationship between pH and antibiotic resistance. An article about persister cells and their relevance to antibiotic resistance. Dr. Levin's faculty website. Dr. Levin's very interesting laboratory website. Intro music is by Reber Clark Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #110: Enumerating the Microbiome October 3, 2025 Today Dr. Sean Gibbons, Associate Professor at the Institute for Systems Biology, returns to the #QualityQuorum to tell us about how he and his colleagues are able to listen very carefully to the microbiome to uncover important hints about health. Host: Mark O. Martin Guest: Sean Gibbons Subscribe: Apple Podcasts, Spotify Become a patron of Matters Microbial! Links for this episode Here is the article from Dr. Norm Pace and coworkers on the showerhead microbiome referenced in the podcast. Here is a nonspecialist summary of Dr. Pace's work on the showerhead microbiome and mycobacteria. Here is a link to a prior episode of this podcast with Dr. Ameet Pinto on microbiology of the water supply. Here is Dr. Gibbon's earlier visit to this podcast. An overview of the difference between microbiome and microbiota. An article about the "misnumbering" of the number of microbial to human cells in people. Here is a nonspecialist summary. An overview of metagenomics. An overview of qPCR. An overview of flow cytometry. Plato's Allegory of the Cave, discussed in this podcast. A cautionary tale about determining a cancer microbiome, as discussed in this podcast. An article by Dr. Gibbons and colleagues described in this podcast about how to estimate microbial biomass directly. An article by Dr. Gibbons and colleagues described in this podcast about how to estimate microbial growth rates in the human gut using metagenomics. An article by Dr. Gibbons and colleagues described in this podcast about how to use metagenomics to determine dietary habits. The website for Dr. Gibbon's research group. The faculty website for Dr. Gibbons at ISB. Courses on microbiome sciences online at ISB. The website for Institute for Systems Biology. Intro music is by Reber Clark Send your questions and comments to mattersmicrobial@gmail.com

Matters Microbial #108: Neanderthal Oral Health, Ancient Bacteria and DNA September 19, 2025 Today, Dr. Laura Weyrich, Associate Professor of Anthropology at Pennsylvania State University, joins the #QualityQuorum to discuss the paleo oral microbiome! We will learn if our ancestors had the same kind of resident microbes as we do. In addition, we will learn about ancient DNA and what it can tell us. Host: Mark O. Martin Guest: Laura Weyrich Subscribe: Apple Podcasts, Spotify Become a patron of Matters Microbial! Links for this episode An obituary for my late and much missed microbiologist friend, Dr. Kimberly Walker. A link to Episode #9 of #MattersMicrobial, with Sebastian Cocioba. The ethics of collecting samples from deceased humans, both ancient and modern. An overview of the efforts to study ancient DNA. Here is another review on that topic. The importance of proper controls for the study of low DNA abundance samples—the famous "kitome" often observed. Here is an article by Dr. Weyrich and colleagues on this topic, as well. A recent article using human bones to detect Yersinia pestis, the causative agent of plague. An overview of the oral microbiome. An article describing how dental calculus can be used to recover ancient DNA. An article by Dr. Weyrich and colleagues describing the human oral microbiome pre and post Industrial Revolution in Great Britain. A video describing our Neanderthal ancestors. An article by Dr. Weyrich and colleagues describing the Neanderthal oral microbiome and related issues. A fine video by Dr. Weyrich describing her research program. Dr. Weyrich's faculty website. Dr. Weyrich's research team website (SO INTERESTING). Intro music is by Reber Clark Send your questions and comments to mattersmicrobial@gmail.com