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The bacteria don't physically reshape the gut themselves. Instead, they work via their hosts. They are more management than labour. Lora Hooper demonstrated this by infusing into germ-free mice a common gut bacterium called Bacteroides thetaiotaomicron-or B-theta to its friends. She found that the microbe actovated a wide range of mouse genes that are involved in absorbing nutrients, building an impermeable barrier, breaking down toxins, creating blood vessels, and creating mature cells. In other words, the microbe told the mice how to use their own genes to make a healthy gut. Scott Gilbert, a developmental biologist, calls this idea co-devolopment. It's as far as you can get from the still-lingering idea that microbes are just threats. Instead, they actually help us become who we are.
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Ed Yong (I Contain Multitudes: The Microbes Within Us and a Grander View of Life)