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Deep Diving

Kristie Nybo, PhD

Gut microbes significantly influence our health, playing roles in everything from brain development to obesity. Will newly engineered synthetic bacteria allow researchers to look inside the intestine to see what’s going on? Find out...

Inside the gut, large communities of bacteria live side by side, mostly peacefully. But small disruptions, such as exposure to an antibiotic or a change in diet, may eliminate not only pathogens but also harmless bacteria, leaving their real estate open to new invaders or vastly shifting the balance of power between microbial strains. This can wreak havoc on the system, affecting not only the bacteria but also the unfortunate owner of that intestine.
Schematic of the memory circuit (1)

While the bacterial population balance can clearly affect intestinal health, recent studies have shown that what lives inside the gut influences functions as wide ranging as brain development, metabolism, inflammation, heart disease, diabetes, and cancer. But the intestine keeps the secrets of its dynamic heterogeneous inhabitants well; just examining it or taking samples can disrupt the balance.

Jonathan Kotula and Jordan Kerns, researchers in Pamela Silver’s lab at Harvard University, set out to develop an agent that could travel through the intestine undercover and report what it had encountered there. To accomplish this, they turned to synthetic biology.

“We used the phage lambda system,” Kerns said. “It’s very well described. It’s a very powerful, stable system. It’s also very simple.”

Together with their colleagues, Kotula and Kerns placed the cI/cro genetic switch, which controls the change between the phage’s lytic and lysogenic life cycles, into the chromosome of a laboratory strain of E. coli to act as a toggle switch. They also included a trigger element to sense the environment.

“I would describe it as the balance between two transcription factors. If you imagine a weight on either side, when one is on, the other is off.” Kerns explained. “The trigger element is a sensing module that interacts [with the environment] and biases the weight of the balance towards one of those states.”

Bacteria in the cI state were introduced into mice, where they traveled through the intestine. In this case, the trigger element was set to detect the antibiotic anhydrotetracycline. In all cases, the bacteria remained in the cI state in untreated mice, and switched to the cro state in mice treated with the antibiotic.

Similar memory switches have been introduced before, but this is the first shown to survive a trip through the intestinal environment. Previously, switches were built within laboratory strains of E. coli, “but because the lab strain has been grown up in lab conditions over the past 60 years, it has lost some of the evolutionary advantages it once had in its natural environment,” explained Kotula.

So the research team isolated an unknown native microbe from the mouse intestine and engineered it to carry the trigger and memory elements. According to Kotula, this native strain functioned just as well as the lab strain but had the ability to survive long term in the gut, while the lab strain was outcompeted by natural gut flora. “In the paper, we showed that it maintains its population out to day 18. We have done subsequent experiments to show that it can go out to about three months.”

“We think this could potentially lead to personalized medicine,” Kotula said. “If these diagnostics are successful in the future, we could isolate a strain from your own personal microbiome, engineer it with the diagnostic elements, and then you would take a probiotic pill with your own bacteria. They would colonize the gut and report on its health.”

The long term goal is to program bacteria to deliver first line therapeutics. For example, a trigger may sense a pathogen, and rather than just switching to the cro state, it would produce a targeted antibiotic to immediately treat the infection without harming the natural flora. For now, the group plans to develop trigger elements that sense biomarkers of inflammation and also to begin working out the intricacies of therapeutic delivery.


Kotula JW, Kerns SJ, Shaket LA, Siraj L, Collins JJ, Way JC, Silver PA. Programmable bacteria detect and record an environmental signal in the mammalian gut. Proc Natl Acad Sci U S A. 2014 Apr 1;111(13):4838-43.

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