Sound-Bouncing Probiotics Will Explore the Gut Frontier

A serving of yogurt delivers millions of helpful bacteria to your gut, but there’s no way to actually see where the microbes go. While that doesn’t affect your yogurt eating habit, it hinders research on developing bacteria-based therapies, which hold great promises for treating everything from immune system diseases to metabolic disorders to perhaps even dissolving cancerous tumors.

But it turns out it might be possible to monitor these elusive organisms inside the body using one of the least sophisticated imaging techniques, according to a new technique described Thursday in the journal Nature.  By genetically engineering bacteria to bounce back sound waves from an ultrasound, researchers were able to make the microbes visible to ultrasound, kind of similar to how submarines are picked up by sonar.  

“The approach is highly innovative and marvelous in its simplicity,” James Collins, a synthetic biologist at MIT who was not involved in the study, told The Daily Beast. The idea may seem simple at first glance, but “its conception did require an insightful leap,” Collins said.

The ultrasound technique could radically expand our ability to track bacteria inside the body and even someday make it to the clinic, helping doctors determine whether disease-fighting bacteria have reached their destination. Currently, researchers can detect bacteria by genetically engineering them to glow green under light. But light can’t penetrate much below the surface of the body, so light microscopy generates blurry images when bacteria are too deep inside. And other techniques that use stronger signals like radiation are too damaging to use in most scenarios.   “Ultrasound is fully capable of looking into the body, and it’s ubiquitous—virtually every doctor’s office has an ultrasound,” Mikhail Shapiro, a chemical engineer at the California Institute of Technology and lead author of the study, said.

To make the bacteria acoustic, Shapiro turned to nature, and found the solution in what is essentially an air bubble. “We came across these really interesting bacterial nanostructures that are called gas vesicles,” Shapiro told The Daily Beast. These gas-filled protein structures are found in water-dwelling bacteria and help the organisms float to the surface to absorb light. Cells filled with these low density air bubbles, Shapiro figured, would reflect sound waves differently than their surroundings, creating ultrasound images with the precision of a hundred micrometers.

All that was needed to do was to find a way to make other bacteria produce the same gas vesicles. But it took the team a few years to figure out how to isolate the genes coding for gas vesicles from aquatic bacteria and transplant them into the genome of bacteria that are actually of interest to humans, for example, a special strain of Escherichia coli that treats some forms of gut infection.

“On the surface it seemed like a simple task. In our case it turned out quite challenging,” Shapiro said.  

Gas vesicles are built by 11 different genes, some of which produce proteins that make up the bubble’s membrane and some help assemble the structure. After a series of mixing and matching of genes isolated from two different organisms, the team arrived at the right combination. The result was a stitched fragment of DNA that once implanted into E-Coli, made the cells produce vesicles large enough to be detectable by ultrasound.

To see if the bacteria are indeed visible even when inside the body, the researchers placed them into the colon of mice and found that ultrasound can indeed pick up the exact location of the mutant bugs inside the intestinal tract. Light microscopy, in contrast, produced fuzzy images.

“We do need methods to communicate with tissues deeper than is currently done using optogenetics and multi-photon optical imaging,” George Church, a geneticist at Harvard who was not involved with the study, said. “Current fluorescence microscopy has much better resolution, 20 nanometers versus 100 microns for ultrasound, but at short distances of 10 microns versus many centimeters for ultrasound.  With the growing role of microbes in therapeutics, monitoring via ultrasound may be of growing interest.”

For now, the approach may be best suited for animal research, helping expand our understanding of the microbiome, said Collins, who is a scientific co-founder of Synlogic, a Massachusetts based company that develops medicinal bacteria. “I do plan to explore the possibility of using this new technology in my academic research.”

Besides spying on bacteria in the guts, the technique could also be used in cancer diagnostics and therapies. To test the idea, the researchers added the gas vesicle building gene to Salmonella Typhimurium bacteria, which is being investigated in cancer research for its ability to invade cancer cells and potentially deliver tumor-killing drugs. They were able to clearly see the bacteria in ovarian tumors inside the body of the mice.

The technique could help to peer into the brain, arguably the hardest-to-crack black box of the body. With a grant from the NIH’s Brain Initiative, Shapiro is working on developing a way to add acoustic properties to neurons so they can be monitored using ultrasound. The challenge, however, is great, he said. “Transplanting genes from one type of bacteria into another has one level of difficulty, to do that from bacteria into mammalian cells like neurons is an order of magnitude more difficult, because of the ways gene expression is handled differently in these types of cells.”

That differs greatly from how we presently monitor neurons inside a living brain using a similarly innovative technique that makes use of green fluorescent protein (GFP), first discovered in glowing jellyfish found off the west coast of the United States. That discovery, which was awarded the 2008 Nobel Prize in Chemistry, revolutionized medical and biological sciences by providing a way to track the activities of proteins within living cells and tell cells like neurons apart in brain tissue.

Only time can tell if sound-reflecting bacteria will have the same impact, but Shapiro welcomes the idea. “Growing up, my scientific hero was Roger Tsien,” one of the three scientists who shared the Nobel for fluorescent imaging, Shapiro said. “If we can have 1/100th the impact on ultrasound that GFP had on fluorescent imaging, I’ll be a very happy person.”