Synthetic
biologists at Rice University have engineered gut bacteria capable of sensing
colitis, an inflammation of the colon, in mice. The research points the way to
new experiments for studying how gut bacteria and human hosts interact at a molecular
level and could eventually lead to orally ingestible bacteria for monitoring
gut health and disease.
The
research, published in a new study in Molecular Systems Biology, involved a
series of breakthroughs in the lab of Jeffrey Tabor, assistant professor of
bioengineering and of biosciences at Rice, and key contributions from
collaborators Robert Britton and Noah Shroyer at Baylor College of Medicine.
Tabor's team, including lead co-author and postdoctoral researcher Kristina
Daeffler, identified the first genetically encoded sensor of a novel biomarker
linked to inflammation, inserted the genes for the sensor into a well-studied
gut bacterium and collaborated with Shroyer and Britton to use the engineered
bacteria to detect colon inflammation in mice.
"The
gut harbors trillions of microorganisms that play key roles in health and
disease," Tabor said. "However, it is a dark and relatively
inaccessible place, and few technologies have been developed to study these
processes in detail. On the other hand, bacteria have evolved tens of thousands
of genetically encoded sensors, many of which sense gut-linked molecules. Thus,
genetically engineered sensor bacteria have tremendous potential for studying
gut pathways and diagnosing gut diseases."
Synthetic
biologists like Tabor specialize in programming single-celled organisms like
bacteria in much the same way an engineer might program a robot. In particular,
Tabor's team is working to develop bacterial sensors that can detect disease
signals in the gut. Like electrical engineers who build circuits from wires and
electronic components, Tabor's team uses genetic circuits to program
single-celled creatures to carry out complex information processing.
Previous
work has suggested that alterations to the gut microbiota, genetic
predisposition and other environmental factors may play key roles in
inflammatory bowel disease, a condition that includes Crohn's disease and
ulcerative colitis and which affects as many as 1.6 million Americans.
"Based
on a number of previous studies, we hypothesized that the molecule thiosulfate
may be elevated during colitis," Daeffler said. "It has been
difficult for scientists to study this link because there aren't tools for
reliably measuring thiosulfate in living animals. Our first goal in this
project was to engineer such a tool."
From
the outset of the project in 2015, Daeffler said, the idea was to use sensor
bacteria, in this case an engineered form of Escherichia coli, to sense
thiosulfate and related sulfur-containing compounds that may also be biomarkers
of colitis. There were well-understood methods for programming E. coli to
produce a fluorescent green protein in response to specific stimuli, but there
were no known genes -- in any organism -- that were used to sense thiosulfate,
and few for the other compounds.
"There's
a link between gut sulfur metabolism and inflammation, and we knew that we
needed to be able to measure sulfur metabolites accurately to diagnose colon
inflammation," she said.
Tabor
said study co-author Ravi Sheth, an undergraduate researcher in the group in
2015, used a computer program to identify potential sensors of thiosulfate and
other sulfur compounds in the genome of Shewanella, a type of bacteria that
live in marine sediment. Tabor's group believes that Shewanella likely breathe
these molecules and use the sensors to turn on the proper enzymes in their
presence.
Daeffler
spent one year engineering E. coli to express the sensor genes, validate their
function and optimize them to respond to the potential biomarkers by producing
a green fluorescent protein signal. It took another year to prove that the
system worked and detected colon inflammation in mice.
The
researchers administered orally two drops containing about a billion sensor
bacteria to both healthy mice and to mice with colitis. They measured the
activity of the sensor bacteria in each group six hours later. The tell-tale
green fluorescent protein showed up in the feces of the mice. Though it was not
visible to the unaided eye, it could easily be measured with a standard
laboratory instrument called a flow cytometer.
The
team found that the thiosulfate sensor was activated in the mice with
inflammation, and was not activated in the healthy mice. Furthermore, the
researchers found that the more inflammation the mouse had, the more the sensor
was activated.
Tabor
said the study shows that gut bacteria can be outfitted with engineered sensors
and used to noninvasively measure specific metabolites and that this result
could open the door to many new studies that could help elucidate a wide range
of gut processes.
Though
it would likely take several additional years of development, and it remains
unknown if thiosulfate is a biomarker of human colitis, the sensor bacteria
might eventually be re-engineered to function as a diagnostic of human colitis,
Tabor said. In particular, the green fluorescent protein could be replaced with
an enzyme that makes a colored pigment.
"We'd
like to develop a home inflammation test where a person prone to colitis
flare-ups would eat yogurt that contained the engineered bacteria and see blue
pigment in the toilet if they were sick," he said.
Tabor
said such a test could reduce unneeded and costly trips to the doctor and
unneeded colonoscopy procedures, which are both expensive and invasive. He said
his team has begun collaborations with gastroenterologists at Baylor to achieve
this goal.
See:
Kristina N‐M Daeffler, Jeffrey D
Galley, Ravi U Sheth, Laura C Ortiz‐Velez, Christopher O Bibb, Noah F
Shroyer, Robert A Britton, Jeffrey J Tabor. Engineering
bacterial thiosulfate and tetrathionate sensors for detecting gut inflammation. Molecular Systems Biology,
2017; 13 (4): 923 DOI: 10.15252/msb.20167416
Posted by Dr. Tim Sandle