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Why scientists are trying to reboot the gut (Includes first-hand account)

Each of us is home to about 100 trillion (that’s with a t) bacteria — about five pounds by weight.

But biologists aren’t just trying to come up with creative methods of eliminating multiple resistant strains of bacteria. Other scientists are busy contriving ingenious ways of turning bacteria into our allies by engineering them for diagnostic and therapeutic purposes. The microbiome is now believed to influence digestion, cognition, mood and the immune system — usually for good. But maybe it can be made to do even more. That possibility has spurred researchers like Pam Silvers and colleagues at her lab at the Systems Biology department of Harvard Medical School to see whether they could do something of breathtaking ambition — “reprogram the microbiome.”

Silver recently presented her findings at the second annual Synthetic Biology: Engineering, Evolution & Design (SEED) Conference in Boston. Synthetic biology is a multidisciplinary science that combines biology and engineering.

It’s true that microbiomes are being reprogrammed all the time — by our diet, our environment, the state of our health, even by the people we kiss, although it has to be intimate kissing and require an “almost constant bacterial exchange… to maintain a shared salivary microbiota.”

What synthetic biologists are talking about, though, involves purposeful reprogramming of the microbiome. “We want to reboot the gut microbiome,” Silver told conference attendees, “We can make natural gut bacteria talk to one another and form a community” — a community that would carry out the program humans have written for it. In her view, bacteria constitute the “black box” of synthetic biology. “Bacteria can sense an event, they can count, they can tell cells to die” – they are “biological computers.” As these engineered bacteria travel through the gut they could potentially “read” it, recording, for instance, whether we’ve been exposed to certain drugs or infections. Once eliminated from the body, the excretion would contain vital information that they’ve picked up along the way, possibly conveyed with a dye that would turn different colors depending on what infections we experienced in the past. That would mean that bacteria could act as diagnostic tools that are far more precise than those currently in use. But why stop there? Bacteria could also be engineered to secrete certain substances that combat inflammation. Such engineered bacterial therapeutics could be used to target Salmonella, for instance, a bacterium which infects about 1.2 million Americans and kills over 400 every year.

The objective is to create non-drugs that act like drugs, but which are both more efficient and precise than conventional drugs. Silver concedes that experiments along these lines are still in their infancy and haven’t progressed beyond animals. But animals may also be beneficiaries of these non-drug drugs, and not just act as experimental subjects. Therapeutics of the kind that Silver and other researchers envision could also prove useful in livestock like chickens, which are especially vulnerable to bacterial infections because of the tight conditions under which they’re kept, allowing for rapid transmission. “I never thought I’d be working with chickens,” she says, “but it turns out that I like chickens, I really do.”

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