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Your gut-microbial ecosystem is a pharmaceutical cornucopia

Your trillions-strong ecosystem of gut microbes, in addition to its many other responsibilities, operates as a homespun pharmaceutical factory.

You undoubtedly know by now that trillions of microbes inhabit every healthy human's large intestine, and that disturbances in these microbial populations can wreak significant effects on our health. But did you know that this ecosystem within you — what scientists call your microbiota — also hums along as a veritable homespun pharmaceutical factory?

Here's the opening sentence in my new Stanford Medicine article, "The Doctor Is in ... Your Gut":

Think of the trillions of bacteria that live inside your gut as a medicine cabinet. The microbial ecosystem thriving in your intestine — what scientists call your gut microbiota — squirts druglike quantities of bioactive chemicals into your bloodstream every single day. Wouldn’t it be nice if you could tailor their output to fit your prescription?

In my article, I report on the progress that Stanford's all-star cast of microbe sleuths Michael Fischbach, PhD; Dylan Dodd, MD, PhD;  Justin Sonnenburg, PhD; KC Huang, PhD; Denise Monack, PhD, and other researchers are making in ferreting out and characterizing specific pharmacologically active substances made by specific bugs in our gut, how these substances affect us for better or for worse, and how ultra-precise tweaking of these bugs' genomes may soon become a practical way of improving our health.

"Manipulating our gut microbiota is hardly a new idea. People have been eating yogurt for millennia," I wrote. But infusions of yogurt and kindred probiotics are no substitute for the coordinated collaboration of a community of one-celled chemists:

To begin with, we really don’t know which microbes would be ideal candidates for gut-microbiota membership. The varying composition of people’s gut microbiota, and the resulting difference in metabolic dynamics underway in different people’s guts, could complicate such simple designations. But say we did know . ... The [pre-existing microbial community's stable grip on our intestinal territory] makes it tough for even the most desirable of [novel] microbes to take root. It’s never easy for a new kid moving into a new neighborhood already populated by battle-tested, streetwise residents who know their turf and know how to get exactly what they need, when they need it and who to get it from.

So it’s not surprising that probiotics are typically transient — within a day or two those freshly introduced bugs are already out of your system — or that their effect tends to be small and not highly predictable.

A distant destination for the speeding bullet train of increasing precision in scientists' understanding of the human microbial ecosystem: The designer microbiota — a set of modular, modified gut-bug communities, each tailored to combat a particular type of health problem, that can be transplanted into people with ailments ranging from heart disease to kidney failure to irritable bowel syndrome and more.

Illustration by Mike McQuade

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