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Scientists want to replace lab workhorse E. coli with the world’s fastest-growing bacterium

A scanning electron micrograph of E. coli bacteria.

Rocky Mountain Laboratories/NIAID/NIH

Scientists want to replace lab workhorse E. coli with the world’s fastest-growing bacterium

One month after being outed as the co-organizer of a controversial project to synthesize the human genome, Harvard University geneticist George Church is now looking to rock the microbiology world. In a preprint article published online this week on bioRxiv, he and colleagues propose an alternative to the workhorse research organism Escherichia coli. They argue that scientific experiments are unnecessarily prolonged by waiting for E. coli to grow and reproduce. As a new model prokaryote—and a potential maker of medicines and other compounds— the team offers Vibrio natriegens, a salt marsh denizen that is the fastest-growing bacterium known.

Since its discovery 131 years ago, E. coli has become the go-to bacterium for fundamental explorations of microbiology, analyses of gene function, and much more. E. coli’s favored status comes from its ease of cultivation and its safety—the four strains commonly used as model organisms have adapted well to growing in laboratories over decades of use, and they have lost their ability to infect the human intestines. They also reproduce relatively quickly, doubling in number every 20 minutes in their ideal growth medium. But the biggest factor driving their popularity is inertia—E. coli is a reliably known bacterium with a long history of documentation.

“We use E. coli just because we know the most about it,” says Harvard geneticist Henry Lee, who collaborated with Church on the Vibrio proposal. Coming from the field of electrical engineering, Lee was dismayed at how much time was spent in genomics research simply waiting for things to grow. This drove him to look for a better alternative, and he landed on V. natriegens, a bacterium that doubles in number every 10 minutes in ideal conditions, compared to twice the time in E. coli and 12 to 16 hours in the bacterium that causes tuberculosis.

V. natriegens shares a genus with Vibrio cholerae, the bacterium behind cholera. However, there’s no evidence V. natriegens itself is harmful to people, Lee says. During testing, it was not susceptible to the same viruses, known as bacteriophages, that cause other Vibrio bacterium to produce the cholera toxins.

To encourage V. natriegens’ adoption and testing by other labs, Lee and his team have sequenced its full genome for the first time, making it—along with a list of tested growing conditions for the bacterium—public. They’ve also developed a version of the CRISPR genome-editing system that works on the bacterium. “We want to develop tools that would make it a drop in, turn-key alternative for E. coli,” Lee says.

The microbiology world seems cautiously intrigued by Lee and Church’s proposal. Columbia University biologist Harris Wang, who uses E. coli to study synthetic biology and genomes, says that further research needs to explore how stable the organism’s genome will be over generations of experimentation and how the salty growing conditions of V. natriegens might affect extracting purified DNA from the microbes, a common step in many studies. “Nonetheless, I think it’s an exciting area to explore and certainly a useful platform if these and other considerations are addressed in the future,” Wang says.

Biologist Richard Lenski at Michigan State University in East Lansing, who has charted the long-term evolution of a batch of E. coli for more than 28 years, also sees promise in V. natriegens, though he’s unsure how much researchers will actually benefit from its reproductive prowess. “I don't know whether most research and applications are really limited by rapid growth, once you're already down into the range where cultures easily replace themselves in a day,” Lenski says. “But time will tell, and it will certainly be interesting to learn more about this organism.”