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Engineering Edible Bacteria

Synthetic biology could yield microbes that fight cavities and produce vitamins.
November 10, 2008

Probiotics, a field that seeks to use edible bacteria to improve human health, may soon undergo a metamorphosis. Students at MIT and Caltech are using the techniques of synthetic biology to create bacteria that fight cavities, produce vitamins, and treat lactose intolerance, as part of the International Genetically Engineered Machines (iGEM) competition at MIT. The new research might lead to a cheaper way to produce medicines or improve diets in the developing world.

Plaque-busting bugs: Students from MIT are engineering the bacterium Lactobacillus bulgaricus (shown here in brown), found in yogurt, to prevent cavities.

Synthetic biology is the quest to design and build novel organisms that perform useful functions. Much research in the field has concentrated on using bacteria as a factory: one of its early successes was the development of microbes that produce malaria medicine. Other research has investigated targeted delivery vehicles, such as microbes engineered to bring medicine to a specific part of the body. But the new projects are attempts to enhance the health benefits of edible bacteria.

These projects capitalize on the fact that our bodies are already colonized by billions of bacteria. “If you really want to apply a bacterium to a person, think about where they naturally exist and survive in a human while still trying to engineer new functions,” says Christina Smolke, a synthetic biologist at Caltech who advises the university’s team.

Our mouths, for example, are a haven to bacteria, both good and bad. Bacteria that live in the dental plaque, called Streptococcus mutans, feed off of sugar on our teeth and then excrete acids, which wear away dental enamel and cause cavities. To create cavity-fighting microbes, the MIT team started with a peptide–a short protein segment–that has been previously shown to prevent the bad bacteria from sticking to the teeth. The team built a piece of DNA containing both the gene that makes the peptide and a gene for a molecular signal that causes the bacterium to excrete it.

The next step will be to insert this piece of DNA into Lactobacillus bulgaricus, a microbe common in yogurt. The students haven’t done that yet, but they have successfully introduced foreign DNA into the microbe, which primes the microbe for further genetic engineering. That in itself is an impressive feat, given that Lactobacillus bulgaricus is not commonly used in the lab and thus requires development of new experimental techniques.

If the microbe can be successfully engineered, eating yogurt would deposit it on the teeth, where it would produce the protective peptide. “This would probably be more effective than an antibacterial that kills everything,” says Chia-Yung Wu, a biology graduate student at MIT who advises the team. “It just targets the harmful stuff.” (A common problem with antibiotics is that they kill both harmful and helpful bacteria in the mouth and gut, leaving an open landscape for bad bacteria to colonize.)

One central project in synthetic biology is the attempt to create a huge, publicly accessible “parts list,” a catalogue of gene sequences and the functions of the resulting proteins. The MIT team doesn’t intend to develop a product for commercial use, but the biological parts that it creates might one day be used in other applications–enhancing the nutritional value of yogurt, for example, with bacteria that produce a specific type of vitamin. The team, which includes undergrads Sara Mouradian and Derek Ju, has already deposited the parts that it’s created in a central repository at MIT called the Registry of Standard Biological Parts. Expanding the registry is one of the most important aspects of the competition. “This year, we sent out 2,000 DNA parts to each team, and we’re getting back 1,500 new parts,” says Randy Rettberg, iGEM director and a principal research scientist at MIT.

The Caltech team focused on microbes in the gut, aiming to create a microbial solution to lactose intolerance. “Rather than taking a daily vitamin, you could drink some gut microbes and be set for a week or month or however long the microbes last,” says Josh Michener, a Caltech graduate student who advises the team.

People who can tolerate dairy naturally secrete lactase, an enzyme that breaks down lactose, a sugar in milk. The breakdown products, which include glucose, are then absorbed into the blood from the small intestine. In people who are lactose intolerant, the sugar is passed to the large intestine, where it is eventually metabolized by a chain of bacteria. In the process, the microbes produce hydrogen and methane gas, the culprits behind the troublesome symptoms–nausea, bloating, gas, and diarrhea–of the disorder.

Lactase pills are available to help people digest milk products, but the Caltech students wanted a more permanent solution. They started with a strain of E. coli often used as a probiotic in Germany. The strain, called Nissle 1917, was originally extracted from soldiers in World War I who were immune to an extreme gastrointestinal virus that swept through an army camp, says Michener.

The students added three biological parts to the Nissle bacterium: a gene that produces the lactase enzyme, a receptor that recognizes lactose, and a sensor that causes the cell to break open at a certain concentration of lactose. With this system, bacteria in the gut would constantly produce lactase. When the receptors on a bacterium’s outer surface bound to a sufficient amount of lactose, they would trigger the explosion of the cell, releasing lactase into the intestine to break down the sugar. The students have so far created the first two components but are having trouble designing the microbes to self-destruct in the proper manner. The team is also working on an edible microbe that would produce folate, a vitamin important for preventing birth defects.

Both teams presented their research at the iGEM competition at MIT this weekend, along with more than 70 other teams from universities around the globe. In past years, students have created everything from bacterial photographic film to banana-scented bacteria and tiny boxes made of DNA.

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