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The “Ideal” Microbiome Is a Myth

Illustration for article titled The “Ideal” Microbiome Is a Myth

Embracing the complexity of the microbiome means doing away with pat conceptions of its function.


Your body is a habitat to trillions of microscopic organisms known, collectively, as your microbiome. Today, the microbiome is one of the hottest areas of biological research, and for good reason. This body-wide ecosystem not only adapts to our diets, lifestyles, and medications, it's also been shown hold sway over our health. The implications for personalized medicine seem clear – the more we understand about the microbiome, the more we can do to condition, or control it to our liking.

But to what end? To shepherd one's microbiome toward some idealized state of healthiness would first require that such a state exists. What does such a state look like? Nobody knows, because an ideal microbiome is almost certainly an illusion. As science writer Ed Yong opines in today's New York Times, contrary to claims by the probiotic industry and the booming genre of microbiome diet books, any system as "complex, varied, ever changing and context-dependent" as the microbiome will, by its very nature, resist easy categorization:

The microbiome is the sum of our experiences throughout our lives: the genes we inherited, the drugs we took, the food we ate, the hands we shook. It is unlikely to yield one-size-fits-all solutions to modern maladies.

We cling to the desire for simple panaceas that will bestow good health with minimal effort. But biology is rarely that charitable. So we need to learn how tweaking our diets, lifestyles and environments can nudge and shape the ecosystems in our bodies. And we need ways of regularly monitoring a person's microbiome to understand how its members flicker over time, and whether certain communities are more steadfast than others.


Read the rest of Yong's smackdown of bad microbiome science in today's New York Times. For more of this, see UC Davis Biologist Jonathan Eisen's ongoing "Overselling the Microbiome" award series. Finally, complement with "Is It Really Worth Having Your Gut Bacteria Tested?"

Top image by Lauren Davis, source materials viaShutterstock

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Jane *is* the... blue passport

Funnily enough, I'm currently falling behind on taking a Coursera course on the human microbiome. I'm not far enough along to see what implications / medical advances they are pushing for; but my own instinct is that my microbiome is a part of my own ecosystem; connected to my surroundings, environment, diet, and so on. There is no use or reason for me to have the microbiome of someone living in L.A. on a vegetarian diet, for example.

It has been found (in mice) that different diets promote or inhibit certain gut bacteria [section1.3], but I am very hesitant to say this is a bad thing. Another note on the course was that the gut bacteria of a human population that ate seaweed had specific genes for digesting seaweed. Which is pretty helpful in that situation.

The problem comes, I suppose, when we need to fix our ecosystem after damage or illness. Then it would be helpful to know what our own normal state should be rather than using an inappropriate "template". I try to grow and eat fruit and veg with minimal processing, or even washing, on the theory that it's a good source of local bacteria for me.