Category Archives: Ecology

Where Did the Term ‘Core Microbiome’ Come From?

In an excellent post about the vaginal microbiome (the microbes that in the vagina), Dr. Rad asks: I wonder if the idea of a ‘core microbiome’ came from Lourens Baas Becking’s oft-quoted idea in microbial ecology that ‘Everything is everywhere, … Continue reading

Posted in Ecology, Genomics, Microbiology, Microbiome, Uncategorized | 4 Comments

A Handy Transformation for Microbiome Data

Handling non-normal frequency data that also have zeros.
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Posted in Ecology, Microbiome, Statistics | 10 Comments

The E. coli O104:H4 Outbreak Gets More Confusing–and Potentially More Disturbing

I engage in some speculation, and hope that I’m very, very wrong.
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Posted in Agriculture, E. coli, Ecology, Microbiology, We're Really Fucked | 4 Comments

Are Shiga-Toxin Phages E. coli Diseases? (File Under Speculative Hypotheses)

Or maybe wild-ass speculation.
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Posted in E. coli, Ecology, Evolution, Genetics, Viruses | 4 Comments

When Economists Misunderstand Biology

And why it matters: we need economists to be better economists.
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Posted in Ecology, Economics, Evolution, Philosophy Shit | 44 Comments

I, For One, Welcome Our Gammaproteobacterial Arsenic-Using Overlords: Why Old School Microbiology Still Matter

This paper demonstrates the need for culturing organisms. That’s something we should emphasize when we train students and post-docs.
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Posted in Aliens! I Seen 'Em!, E. coli, Ecology, Genomics, Microbiology, Microbiome, NASA, News Media

Some Thoughts About the Statistics of the Human Microbiome

Big critter ecologists have thought about this kind of data for decades, and we should learn from them.
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Posted in Ecology, Microbiome, Statistics | 8 Comments

The Great Mortification of Economics: What Happens When Natural History Is Removed

Ignoring history and indulging physics envy in an attempt to glimpse the Economic Godhead.
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Posted in Ecology | 13 Comments

‘Hopeful Monsters’: Nothing in Evolution Makes Sense Except in the Light of E. coli (and Shigella)

Bacterial evolution muddies up the water.
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Posted in E. coli, Ecology, Evolution, Genetics, Genomics, Microbiology, Plasmids | 2 Comments

Methicillin Resistance in MRSA: Evolve and Spread Locally, Not Globally?

For at least one clone of MRSA, it looks like there isn’t pandemic spread of a resistant clone, but, instead repeated gene transfer into a highly prevalent sensitive S. aureus background.
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Posted in Antibiotics, Ecology, Evolution, Microbiology, MRSA | 1 Comment