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

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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

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