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

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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 [email protected]

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

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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 [email protected]

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

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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 [email protected]

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

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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 [email protected]

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

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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 [email protected]

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

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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 [email protected]

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

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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 [email protected]

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

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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 [email protected]

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

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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 [email protected]

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

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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 [email protected]