Engineered Safeguards for Synthetic Probiotics

by Katherine Collins

Newton South High School, Newton, MA

First Place

The thirteen-year old boy was wheeled on his gurney into the operating room. He needed a colonoscopy: after months of incessant bloody diarrhea and distressing uncertainty regarding his ailment, his doctors finally decided that he had had enough and signed the freshly-minted teenager up for the uncomfortable procedure. Due to his predicament, the boy had lost close to 40% of his blood, shed 16 pounds of his already svelte frame, and was no longer able to participate in the sports he adored. Life grew dismal, and the post-colonoscopy diagnosis of ulcerative colitis set him up for a tough cycle of medications and unwarranted side-effects. Two subsequent bouts of a C. difficile bacterial infection left him a shell of his past self. Only an incredibly restrictive dietary regimen and an overwhelming onslaught of daily pills were able to lift him out of such a deep, dreary hole. But, why did my younger brother have to plummet to such a painful state in the first place? And why has modern medicine not come up with less intrusive diagnostic procedures and demanding drug therapies for conditions like ulcerative colitis?

The blossoming field of synthetic biology may soon offer exciting options and potential solutions to these pressing challenges. Synthetic biology is a new field at the interface of engineering and biology, developing new biotechnologies such as synthetic probiotics to combat a range of harsh diseases including inflammatory bowel disease (IBD) — my brother’s condition — as well as bacterial infections like those caused by C. difficile. Synthetic probiotics, consisting of engineered microbes condensed into the form of a pill, are paving the way for entirely new classes of medications. For example, microbes are being designed to sense inflammation and produce anti-inflammatories directly at the site of inflammation in IBD patients. By detecting and remediating inflammation in a targeted fashion, therapeutics such as these could render colonoscopies inconsequential, saving kids like my brother much agony, worry, and potentially, embarrassment. Moreover, an effective synthetic probiotic pill could reduce the number of needed daily medications from 20 to merely one.

Yet, with such hope and potential, why is it that these revolutionary living diagnostics and therapeutics have yet to hit the market and become commonplace in mainstream medicine? Uncertainty and concern regarding the engineered organisms’ potential interactions with a patient’s body, as well as with the surrounding environment, pose barriers for the prospect of synthetic probiotics’ emergence in the real world.

Synthetic probiotics could dramatically improve the quality of life for those affected by inflammation-related diseases like my brother; however, if implemented carelessly, the pills could pose devastating health effects to well-meaning patients. Imagine taking a pill intended to do good, but it largely does harm. What if you have an adverse reaction to the synthetic probiotic? How would you get the live, engineered microbes out of your body? And what about the large variance in individuals’ microbiome composition — what if the newly administered bacteria do not interact with the patient’s communal microbes as predicted? Synthetic biologists are tackling these important challenges through responsible engineering, designing and endowing synthetic probiotics with programmable kill switches, stringent biocontainment mechanisms that allow one to readily remove the microbes from a patient’s body on demand as desired.

Programmable kill switches typically consist of synthetic biological circuits that regulate the intracellular production of a toxin that, if present, will immediately kill the microbe. These switches are usually set in the “off state” (that is, no toxin is produced), enabling the synthetic probiotics to go about their intended business, acting as living diagnostics and therapeutics. Importantly, these switches can be flipped to the “on state” (where the toxin is produced) by a small molecule such as a drug or metabolite. In this way, if the patient has a bad reaction to the synthetic probiotic, he or she can simply take the “on-switch” safety pill and wipe out the synthetic probiotics. This example of responsible engineering ensures the well-being of the patient, protecting them from unintended harm.

But preventing harm to the recipient of the synthetic probiotic is only one of the concerns surrounding this new biotechnology. Imagine if the engineered organisms leaked or escaped into the environment. How would they affect our water or food supply? Could they be transmitted to other unsuspecting people, causing unanticipated reactions? Imagine the domino effect that these engineered microbes could have on nature’s fragile ecosystems, potentially wiping out or altering entire species. Synthetic biologists have side-stepped this dilemma by creating a second biocontainment mechanism known as engineered auxotrophy. Auxotrophs are bacteria that cannot produce all of the amino acids essential to their survival, and must instead rely on external sources for these missing amino acids.

Synthetic biologists have harnessed this effect and created engineered auxotrophs by introducing modifications to the genome of the bacteria composing the synthetic probiotics. Specifically, synthetic biologists have reprogrammed the DNA of the engineered microbes to ensure that the synthetic probiotics cannot produce all of their needed amino acids and must rely on ones that are only produced in the human body. In this way, if the synthetic probiotics leave a patient’s body and escape into the environment, they will not be able to survive — they will starve and die. In essence, this biocontainment mechanism programs the microbes to self-destruct once they exit a patient’s body. Thus, engineered auxotrophy is a clever way to ensure that synthetic probiotics do no harm to the broader environment.

Although this solution decreases the productivity of synthetic probiotics and increases their production cost, extra time and money are sometimes necessary concessions if engineers want their technology to meet environmental sustainability criteria and keep the public safe — a prime example of responsible engineering in action. Responsible engineering is about finding potential weaknesses and sources of harm within a technology and then modifying that technology to ensure that the weakness is remediated. Synthetic biologists are doing just that through engineering auxotrophs, regardless of productivity and fiscal losses.

Ultimately, the advent of programmable kill switches and engineered auxotrophy represents important strides towards attaining responsible engineering in the field of synthetic biology. Synthetic probiotics offer tremendous potential — my brother needs them desperately, as do countless other sufferers of inflammatory conditions such as asthma, allergies, or IBD, that prevent them from living their lives to the fullest extent. Such probiotics could dramatically improve the quality of life and health of many individuals, and thanks to engineered genetic safeguards, these new technologies will hurdle the challenge of maintaining the health and well-being of the host and surrounding environment, and transitively, that of the public at large. Thus, it looks probable that in the future, unfortunate teenagers will not have to suffer through repeated, failed medications, intrusive operations, nor the embarrassing trauma of persistent bloody diarrhea; rather, they will be able to pop a pill developed by responsible bioengineers and squelch the source of their ailments.

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