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

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• 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

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Today Dr. Liz de Ora Ortiz, postdoctoral scholar in the Secor Laboratory at Montana State University, joins the #QualityQuorum to discuss a fascinating new technology that allows investigators to follow bacteriophage infections in live animals.

Host: Mark O. Martin

Guest: Liz de Ora Ortiz

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• The fascinating and frustrating (for researchers like me) story of Vampirococcus.
• A Vampirococcus summary for new #Micronauts.
• An overview of Agrobacterium, a bacterium about which all micronauts should know (think about genetic engineering in agriculture!).
• The story of Pelagibacter, very probably the most abundant organism on Earth.
• The story of Akkermansia, and its impact on metabolic health and the gut microbiome.
• An important essay by the late Dr. Elio Schaechter regarding paradigm shifts in microbiology. Much recommended!
• A truly wonderful video about bacteriophages and their importance.
• A simple video explaining the life cycle of lytic and lysogenic bacteriophages.
• A video from the American Society of Microbiology linking CRISPR and bacteriophages.
• A review of genes "hitchhiking" in bacteriophages.
• An introduction to Phollow technology.
• An overview and discussion of the Phollow technology discussed in this podcast (paywalled).
• A Phollow related publication also discussed during the podcast.
• The Wiles laboratory, where Dr. de Ora Ortiz and colleagues developed the Phollow technology.
• Dr. Travis Wiles' episode of #MattersMicrobial.
• The Secor laboratory, where Dr. de Ora Ortiz currently works.
• Dr. de Ora Ortiz's LinkedIn profile.

Intro music is by Reber Clark

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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

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• 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 [email protected]

Today Dr. Julia Willett, Assistant Professor in the Department of Microbiology and Immunology at the University of Minnesota, joins the #QualityQuorum to discuss how to investigate unknown genes found in nearly every bacterial genome. Call it Microbial Dark Matter!

Host: Mark O. Martin

Guest: Julia Willett

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• Microbial "Dark Matter"—unknown genes in microbial genomes.
• The process of annotation.
• An article about the "Y-ome" or understanding "uncharacterized" genes.
• The smallest independently growing (and engineered) bacterium, JCVI-syn3.0. It still has many "uncharacterized" but necessary genes.
• An essay on Enterococcus faecalis.
• Diseases caused by Enterococcus.
• The concept of the pathobiont.
• Dr. Arturo Casadevall's thoughts on the term "pathogen."
• The use of transposon mutagenesis to create "knock outs" of bacterial genes.
• Array transposon mutagenesis. Here is an article coauthored by Dr. Willett on that topic.
• The Alpha Fold program for predicting gene function.
• A webinar describing "Microbial Dark Matter" by Dr. Willett.
• Dr. Willett's faculty website.
• Dr. Willett's laboratory website.

Intro music is by Reber Clark

Send your questions and comments to [email protected]

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

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• 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 [email protected]

Today Dr. Gregory Morgan, Professor in the School of Humanities, Arts, and Social Sciences at Stevens Institute of Technology, joins the #QualityQuorum to discuss how cancer causing viruses advanced molecular biology as described in his recent book Cancer Virus Hunters.

Host: Mark O. Martin

Guest: Gregory Morgan

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• Here is a link to Dr. Morgan's book on the topic discussed today.
• A lovely interview with Dr. Morgan about his book.
• A great history of molecular biology, "Eighth Day of Creation" by Horace Freeland Judson.
• The History and Philosophy of Science program at the University of Pittsburgh.
• An overview of the Rous Sarcoma Virus.
• A biography of Dr. Peyton Rous.
• A video describing how RSV causes cancer by "stealing" normal genes.
• How some viruses may contribute to the development of cancer. Here is another video on that topic.
• The field of tumor virology.
• A really wonderful video on the genetic origin for cancer.
• An overview of oncogenes and protooncogenes.
• A video exploring how proto-oncogenes become oncogenes, and can contribute to the development of cancer.
• The concept of "contagious cancer" that is rare but exists.
• The story of papilloma viruses and "jackalopes."
• The history of Cold Spring Harbor Laboratory.
• An overview of retroviruses.
• Retroviruses and FeLV.
• Blue chicken eggs and ancient retroviruses. A summary for novice #Micronauts.
• Mammalian (including human) placenta and ancient retroviruses.
• Nixon's "War on Cancer."
• An overview of the src gene.
• An overview of the ras gene.
• An overview of the p53 gene.
• A video explainer of the enzyme reverse transcriptase.
• A biography of Howard Temin.
• A biography of David Baltimore.
• The story of Human Papillovirus (HPV) and cancer.
• Dr. Morgan's faculty website.

Intro music is by Reber Clark

Send your questions and comments to [email protected]

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

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• 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 [email protected]

Today Dr. Hannah Ledvina, Assistant Professor in the Molecular, Cellular, and Developmental Biology Department at the University of Michigan joins the #QualityQuorum to discuss how bacteria can protect themselves against predators in unusual ways . . . including a type of armor!

Host: Mark O. Martin

Guest: Hannah Ledvina

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• The "Giant Microbes" website.
• A prompt for my course: an article on "Animals in a Microbial World," with so many interesting examples. Here is a summary for novice #Micronauts.
• A prompt for my course: an article by the late, great Lynn Margulis on the nature of kefir grains and the definition of multicellularity and the organism.
• A prompt for my course: an article on hyperpolyploidy in bacteria.
• An explanation of "genomic islands."
• A link to a previous guest of #MattersMicrobial, Dr. Laura Williams, discussing Bdellovibrio and undergraduate based research.
• An overview of predatory bacteria. Here is a more recent overview.
• An overview of the predator Myxococcus.
• A wonderful video showing the predatory process of Myxococcus.
• A fine review of the predator Bdellovibrio.
• A video of the life cycle of Bdellovibrio.
• Some work by Dr. Koval and colleagues suggesting that aspects of the outer cell wall is not involved with resistance to Bdellovibrio.
• Recent VERY exciting work suggesting that there is indeed a receptor on bacteria that Bdellovibrio can recognize. Here is a short summary of that work.
• Could Bdellovibrio become a "living antibiotic"?
• A reminder from Drs. Kolter and Losick that bacteria in the laboratory can be quite different from their relatives in nature.
• The article under discussion on this podcast by Dr. Ledvina and colleagues. Here is an editorial summary on the article.
• An article on curli proteins in bacteria.
• An article on amyloid like proteins in bacteria.
• A video by Dr. Ledvina on the research interests of her group.
• Thoughts on an "immune system" for bacteria.
• Dr. Ledvina's faculty website.
• Dr. Ledvina's research group website.

Intro music is by Reber Clark

Send your questions and comments to [email protected]

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

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• 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 [email protected]

Today Dr. Joshua Shrout, Professor of Civil and Environmental Engineering and Earth Sciences at the University of Notre Dame joins the #QualityQuorum to discuss the work of his research team on sociomicrobiology. This includes how bacteria sense a surface, move together in groups, and communicate with one another.

Host: Mark O. Martin

Guest: Joshua Shrout

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• Here is a wonderful video about the late great Dr. Esther Lederberg. Here is another article on that same subject.
• Here is an article about prodigiosin synthesis and Serratia marcescens.
• An introduction to the concept of sociomicrobiology.
• An overview of bacterial swarming. Here is a wonderful swarming video.
• An overview of bacterial swimming in liquid.
• An article about group/social motility in Myxococcus.
• A fine video explaining the amazing bacterial flagellar motor.
• An article about Vibrio parahaemolyticus and swarming.
• An overview of quorum sensing.
• Bacteria cultivated in the laboratory undergo mutational changes during "domestication."
• Pigments produced by Pseudomonas, including pyoverdin and pyocyanin.
• An article from Dr. Shrout's laboratory group describing interactions between Pseudomonas and Enterococcus described in this episode.
• The Type IV pili-based motility system.
• An article from Dr. Shrout's laboratory describing how Pseudomonas can "walk" on one pole during swarming.
• Here is a video from Dr. Shrout's laboratory showing Pseudomonas "walking" on their poles.
• An overview video of the Shrout laboratory's research interests.
• Dr. Shrout's faculty website.
• Dr. Shrout's truly beautiful research website. There are wonderful microbial videos there. Very much worth your time.

Intro music is by Reber Clark

Send your questions and comments to [email protected]