Optogenetics Approach Delivers Precision Necessary to Study Bacteria in the Gut

Researchers in Texas have succeeded in effectively turning gut bacteria inside the intestines of worms “on” and “off” by applying different colors of light, via an optogenetic control mechanism. The work helped the research team led by Baylor College of Medicine’s Meng Wang and Rice University’s Jeffrey Tabor show that colanic acid (CA), a metabolite, is produced by intestinal bacteria, rather than digested in the stomach.

Previous research conducted by Wang indicated that CA extended the lifespans of worms by as much as 50% — a value that corresponds to more than four weeks in a laboratory environment. The new advance succeeded in restricting CA production to the gut of worms, ultimately allowing the scientists to measure its benefits to the intestinal cells.

In the research, distinctly engineered strands of E. coli made CA when exposed to green light, as opposed to red. By then incorporating genes to make different colors of fluorescent proteins, the method assured that one color would always be brightly, visibly present when viewed microscopically. This allowed the scientists to see where the bacteria were present inside the worms.

Only when the bacteria produced CA did a second color become visible.

Researchers held the bacteria under a red light before feeding them to the worms. As the bacteria moved through the digestive tracts and reached the intestines, they activated green light.

“When exposed to green light, worms carrying this E. coli strain also lived longer. The stronger the light, the longer the lifespan,” Wang said. Wang is the Robert C. Fyfe Endowed Chair on Aging, a professor of molecular and human genetics at the Huffington Center on Aging at Baylor and a Howard Hughes Medical Institute investigator.

In earlier experiments with higher life forms, Wang showed that CA effectively regulated the balance between mitochondrial fission and fusion, in both intestinal and muscle cells. The effect contributes to cellular longevity; mitochondria, the organelles that deliver energy to individual cells, balance between fission and fusion, though their efficiency decreases over time. Mitochondrial dysfunction causes cellular decline as organisms age.

Light-responsive bacteria fed to worms are visible in images of the worms' gastrointestinal tracts. Engineers programmed the bacteria to produce a red fluorescent protein called mCherry so that they would be easy to see under a microscope. When exposed to green light, the bacteria also produce a green fluorescent protein called sfGFP, which causes them to glow green. When exposed to red light, they do not produce the green protein. Worms in the left column were treated with red light. Worms in the right column were treated with green light. Courtesy of Jeffrey Tabor/Rice University.

The results, what they reveal, and the transferability of the research, Tabor said, raised questions as to whether intestinal cells benefit from CA before other cells, due to the fact that CA is produced in the gut. The larger question: Do CA-caused mitochondrial benefits spread throughout the body from the intestines?

The researchers said they did not find evidence of short-term mitochondrial benefits in the muscle cells of the worms. It means the longevity-promoting effect of CA commences from the gut before spreading into tissue. The new technology used light to enable that precise observation, though the accuracy of the technology could allow researchers to answer additional questions about gut metabolism.

“We know gut bacteria affect many processes in our bodies,” Tabor said. “They have been linked to obesity, diabetes, anxiety, cancers, autoimmune diseases, heart disease, and kidney disease. There has been an explosion of studies measuring what bacteria you have when you have this illness or that illness, and it’s showing all kinds of correlations.”

Tabor said the goal is to move toward showing causality, in addition to correlation. Bacteria that one can eat to improve health and/or treat disease is something scientists continue to covet.

Difficulty remains, however, in designing experiments that show what is happening in specific locations inside the gut, thereby charting a course for showing that molecules produced by gut bacteria may cause disease or health.

“The gut is a hard place to access, especially in large mammals,” Tabor said. “Our intestines are 28 feet long, and they’re very heterogeneous. The pH changes throughout and the bacteria change quite dramatically along the way. So do the tissues and what they are doing, like the molecules they secrete.

“To answer questions about how gut bacteria influence our health, you need to be able to turn on genes in specific places and at particular times, like when an animal is young or when an animal wakes up in the morning,” he said. “You need that level of control to study pathways on their own turf, where they happen and how they happen.”

Because it uses light to trigger genes, optogenetics offers that level of control, Tabor said.

“To this point, light is really the only signal that has enough precision to turn on bacterial genes in the small versus the large intestine, for example, or during the day but not at night,” he said.