Matters Microbial

Matters Microbial #123: What Whooping Cough Can Teach Us
February 6, 2026




Today Dr. Seema Mattoo, Associate Professor of Biological Sciences at Purdue University, joins the #QualityQuorum to discuss the fascinating molecular genetics of the bacterium Bordetella pertussis, which can cause the human disease whooping cough.
Host: Mark O. Martin
Guest: Seema Mattoo
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Links for this episode
Here is a link to Tiffany Ard's fine science related art.
CDC information regarding Whooping Cough also called pertussis.
An overview of the causative agent of whooping cough, Bordetella pertussis.
A video about pertussis and its symptoms and treatment.
More detail about B. pertussis and close relatives.
Recent outbreaks of pertussis.
An overview of vaccine development and its history for B. pertussis.
An article about vaccine hesitancy and the return of childhood diseases like pertussis.
Information on "whole cell" versus "acellular" vaccines.
An article discussed today, demonstrating that the same molecule (a fragment of bacterial cell wall peptidoglycan) can be a factor for disease in humans, and facilitate symbiotic light organ development in the Hawai'ian Bobtail Squid
More information of B. pertussis' trachael cytotoxin, or TCT. 
An overview of bacterial effectors interacting with our physiology in general.
The concept of virulence factors.
IgA versus IgG responses to infections.
An overview of Type III Secretion Systems.
An overview of sigma factors in bacteria.
ECFs as  sigma factors.
Partner-switching studies.
Fic genes.
An overview of post translational modification.
An essay on Theodosius Dobzhansky and his famous maxim.
Protein misfolding and disease.
The role of mentorship in science.
The Hypothesis Fund and its aims.
An article by Dr. Mattoo and colleagues discussed today about partner switching and Type III Secretion Systems.
An article by Dr. Mattoo and colleagues discussed today about Fic proteins and adenylation.
An article by Dr. Mattoo and colleagues discussed today about Fic proteins, post translational modification, and Parkinson's Disease.
An article by Dr. Mattoo and colleagues discussed today about AMPylation, Fic proteins, and sensing misfolding in the endoplasmic reticulum.
Dr. Mattoo's faculty website.
The fascinating laboratory website of Dr. Mattoo and colleagues.
Intro music is by Reber Clark
Send your questions and comments to [email protected]

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
 
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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 [email protected]

Matters Microbial #121: Phollowing Phage in the Gut Microbiome
January 7, 2026 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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Links for this episode
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
Send your questions and comments to [email protected]

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
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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 [email protected]

Matters Microbial #119: Investigating Microbial "Dark Matter"
December 22, 2025 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
Subscribe: Apple Podcasts, Spotify
Become a patron of Matters Microbial!
Links for this episode
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]