Designer Microbes: a Potential Living Cure for Crohn's and Phenylketonuria

Oct. 12, 2018

In this third article on MICROBIOtechnology, I'll discuss how synthetic biology and specially designed microbes are being developed to cure diseases.

Treating Disease From A New Angle

The composition of the human microbiome heavily influences host health, immunity, and disease by contributing genes, proteins, and metabolites to the human ecosystem. As scientists attempt to tease apart the contribution of microbes to various diseases, they have found that certain disorders, such as inflammatory and metabolic diseases, are a quagmire of human genetics, environmental stresses, microbe composition, and both human and microbe metabolisms working in concert.
Instead of approaching disease from the human genetics angle, synthetic biologists ask whether they can engineer microbes to inform and treat disease. After all, microbes are essentially tiny single-celled factories that perform various enzymatic reactions within an exceptionally small volume. Could bacteria be re-engineered to perform specific tasks, such as sensing the environment, or create specific products, like drugs, to treat disease? That’s exactly where the field of personalized medicine is going for 2 debilitating disorders that, as of yet, have no cures: the metabolic disorder, Phenylketonuria, and the inflammatory bowel disorder, Crohn’s Disease.

Preventing Toxicity in Phenylketonuria

Phenylketonuria (PKU) is a genetic metabolic disease that causes the body to make insufficient amounts of an enzyme called phenylalanine hydroxylase, which breaks down phenylalanine (Phe) into the essential amino acid tyrosine (Tyr). People with PKU have abnormally high levels of Phe, causing problems by outcompeting with other amino acids essential for brain development from crossing the blood-brain barrier. PKU patients are also deficient in Tyr, necessary for the production of neurotransmitters epinephrine, norepinephrine, and dopamine. This combination of excess Phe and insufficient Tyr causes compounding neurological defects that lead to developmental delays, intellectual disability, and microcephaly (small head size).
One of the ways PKU can be treated is with a strict diet that minimizes Phe consumption while increasing Tyr intake via supplements. Phe is an amino acid found most commonly in high protein foods such as poultry, fish, nuts, egg whites, soybeans, and some dairy products. However- there may be a microbial alternative to the PKU diet in the near future.
Scientists at Synlogic Inc., a biopharmaceutical company in Cambridge, Massachusetts, engineered a non-pathogenic strain of Escherichia coli to produce Phe-metabolizing enzymes in the mammalian gut. So far, results are promising. Activity of the engineered  E. coli strain (SYNB1618) was tested by administration to mouse and primate disease models for PKU. After the animals consumed a high-protein, high-Phe diet, researchers tested the blood levels of Phe. Synlogic was able to show significant reduction of Phe in the blood serum of both species and that the ingested Phe was converted to a byproduct called trans-cinnamate. This molecule was then metabolized by the host to hippurate and harmlessly excreted in the urine. Patients still need to supplement their diet with Tyr pills, but they can avoid the complexity and inconvenience of the PKU diet. Currently, SYNB1618 is undergoing clinical trials, and PKU patients can look forward to the results of Phase 1 and 2 data in 2019.
But PKU patients shouldn’t be the only ones celebrating this achievement. This research may be applied to other metabolic disorders by using E. coli engineered to produce enzymes important for normal human metabolic functions. One such genetic disorder is maple syrup urine disease (MSUD), a disorder in which the branched-chain amino acids leucine, isoleucine and valine cannot be broken down by the body due to a mutation in one of four genes. Though MSUD is slightly more complex than the single gene mutation of PKU, a combination of human genetic testing and bacterial synthesis of the missing gene product could be a promising therapy for this disease.
But what happens when a disease has hundreds of associated gene mutations instead of just 1 or 4, as in the case of the inflammatory bowel disorder Crohn’s Disease?

Combatting Crohn’s: Living Sensors Respond to and Rewire Our Gut

Crohn’s disease, a disorder characterized under the umbrella of inflammatory bowel disorders (IBD), is a painful and debilitating disorder where the body’s own immune system attacks the intestinal lumen. This leads to unpleasant symptoms such as abdominal pain and diarrhea, but can also cause more serious events such as malnutrition, ulcers, bowel obstructions, tears (fissures). Severe Crohn’s Disease cases can lead to the formation of unnatural openings (fistulas) that connect the intestine to other tissues or hollow organs.
Unlike PKU, which is a metabolic disorder stemming from a single characterized gene, inflammatory disorders like Crohn’s disease are significantly more complex: not one single gene or pathogen has been identified as the sole cause. Over 170 regions on the human genome have been associated with an increased risk for IBD, and over 70 of those are associated specifically with Crohn’s Disease. But it’s not all genetics either -- several pieces of evidence suggest that microorganisms affect the pathogenesis of Crohn’s. Some patients improve when put on extended courses of antibiotics, and germ-free animals almost never develop inflammatory bowel diseases. Furthermore, when the intestinal content of an afflicted mouse is transferred to a healthy mouse, inflammation often results.  
How does one begin to attack a problem with a tangled web of hundreds and even thousands of possible causes? David McMillen, a synthetic biologist at the University of Toronto, believes that the answer lies in repairing damaged cells instead of wading through hundreds of underlying genetic and environmental causes.
McMillen is the leader of a Medicine by Design team dedicated to innovating regenerative medicine therapies for intestinal diseases. Based at the University of Toronto, the team is designing a molecule-sensing microbe that can sense inflammation in the gut, switch on drug-production, and regenerate damaged tissue all in one.
That seems like a tall order, but bacteria react and respond to their environments constantly, and McMillen’s team is harnessing that natural cause-and-effect as a new therapeutic. When asked about his team’s ideas of how to fight inflammatory disorders such as IBS and Crohn’s, McMillen told reporters "our ideal outcome would be to be able to deliver a therapeutic into the gut with a programmable bacterium, which you could use for multiple diseases."
A reparative bacterial treatment would be a big improvement over current treatments for Crohn’s disease, which address the disease cause, but with serious risks to patients. Often treatment requires administration of steroids and other anti-inflammatory drugs that suppress the body’s natural immune system. This puts patients in danger of acquiring potentially life-threatening infections (such as Clostridioides difficile, or  C. diff) and greatly reducing patient quality of life.
McMillen’s team is taking advantage of the way that intestinal microbes quickly change their gene expression in response to inflammation. The goal is to identify the relevant gene expression changes and then transform them into inflammation sensors. Once the sensor is established, the team can work to engineer the appropriate response. That’s where the work of McMillen’s collaborator Dana Philpott comes in. Her team determined that intestinal bacteria secrete a molecule called muramyl dipeptide (MDP), which stimulate intestinal stem cells to proliferate and repair intestinal lumen by generating more intestinal cells. Theoretically, "it should be possible to stimulate the human receptor to the right level and promote healing of the cells that are hardest hit during Crohn's disease," Philpott explained.

The Sky Is the Limit Tor Treating a Sick Gut

McMillen and Philpott’s teams are working hard to connect the circuit of cause and effect within one bacterial cell, and they are hopeful not only for their own work but for the precedent this type of work sets for all sorts of disease. (On a more lighthearted note, even hangovers can now be cured by probiotics thanks to an acetaldehyde-degrading Bacillus from Zbiotics.) Though much remains to be determined regarding safety and cost of these microbial drug factories, it is for sure an exciting time to be in the field of synthetic biology.


Move over Silicon Valley, the next big thing is microscopic! Microbes are taking over the biotech industry, contributing their unique characteristics toward a diverse array of applications, technologies, and new startup ventures. From influencing personalized medicine, improving agriculture, and degrading previously undegradable plastics to bioproduction of fuels and 3D printing materials, microbes have infiltrated a slew of industries. No doubt about it, microbiology is the technology buzzword of the year.

Further Reading:

23 And All Of Us: Personalized Medicine Via Microbiome Sequencing
Yeast Through The Years: From Hidden Fermenters To Synthetic Biology
Does A Minimal Genome Exist?
Digesting The Indigestible: How Microbes Are Chewing Up Our Big Plastic Problem

Author: Monika Buczek

Monika Buczek
Senior Contributor Dr. Monika Buczek completed her doctoral research in Molecular, Cellular and Developmental Biology and now works in translational cancer research.