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

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• 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

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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

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• 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

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

Host: Mark O. Martin

Guest: Amir MItchell

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• 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

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

Host: Mark O. Martin

Guest: Reed Stubbendieck

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• 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 [email protected]

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

Host: Mark O. Martin

Guest: Manuel Kleiner

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• 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

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

Host: Mark O. Martin

Guest: Karen Lloyd

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• 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 [email protected]

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

Host: Mark O. Martin

Guest: Rosie ’Anolani Alegado

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• 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 [email protected]

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

Host: Mark O. Martin

Guest: Rachel Poretsky

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• 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

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

Host: Mark O. Martin

Guest: Karen Ottemann

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• 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 [email protected]

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

Host: Mark O. Martin

Guest: Arturo Casadevall

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Become a patron of Matters Microbial!

• 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 [email protected]