Mini Guts Could Improve Personalized Therapy Production

Researchers use minibioreactor arrays to study the gut, coupling them with high-throughput screening techniques to examine the effects of different therapies on digestive system diseases. Reported by

by Melissa Lutz Blouin
April 02, 2018

Gut bacteria play a major role in disease, but understanding the interactions among microbiomes containing more than 1,000 bacterial species, foods, and medications has proven elusive. Virologist Robert Britton and his colleagues at Baylor College of Medicine are addressing this problem with a small system of artificial “mini guts” that recreate the intestinal microbiome.

Britton will use these minibioreactor arrays to study the gut, and to couple them with high-throughput screening techniques to examine the effects of different therapies on digestive system diseases.

Several research groups have already created artificial gut models to grow complex microbial colonies with hopes of studying potential intestinal disease therapies. These continuous flow systems enable researchers to control pH and nutrients while removing waste products and dead cells over prolonged periods while studying gut behavior. Many try to recreate multiple parts of the intestinal tract. Unfortunately, these systems are big, elaborate, and time-consuming to run. Sometimes, the results are difficult to reproduce.

Britton and his colleagues decided to downsize and simplify these gut models in hopes of making it easier to more rapidly identify potential therapeutics.

“Rather than try to replicate a colon, we tried to miniaturize it,” Britton says.

More for You: Harnessing Microbiome Science for Therapeutic Development

The result is an array of six 15 ml minibioreactors positioned over a magnetic stir plate. The system is so small that eight arrays (48 bioreactors) can fit in a single anaerobic chamber at a time. The reactors controlled flow with two 24-channel peristaltic pumps.

In all cases, the minibioreactors successfully grew flourishing microbiota using biopsied fecal material from different patients. The colonies resisted colonization by Clostridium difficile, bacteria that can cause diarrhea and sometimes life-threatening inflammation of the colon. They also revealed physiological differences between different C. difficile strains. The minibioreactors allowed researchers to change many variables over the course of a two-week experiment, introducing antibiotics, disease-causing bacteria, probiotics, and other therapeutics.

Once they had developed a working “mini gut” system, the scientists used it to screen for new therapeutics to inhibit C. difficile. C. difficile often attacks the gut when people are taking antibiotics that kill off beneficial bacteria, and may require multiple and sometimes unsuccessful antibiotic treatment to suppress.

Using the minibioreactor arrays, the researchers recreated an antibiotic-treated miniature version of the gut microbiome and introduced C. difficile to induce infection. In this environment they showed that when activated by glycerol the probiotic Lactobacillus reuteri has antimicrobial properties that can combat the disease-causing bacteria. This could pave the way for a new therapeutic treatment of this disease. The researchers reported their findings in Infection and Immunity.

Despite the small size of the “mini gut” model, the researchers faced some big challenges as they worked to create it. The first was how to handle the liquid; Britton and his team needed a way to pass the media through the chambers and then pass the waste out. They initially had leaks due to clogs in the system and had to adjust the tubing. Then they discovered another problem along the way.

“A lot of these microbial communities produce hydrogen sulfide, which does not play well with some materials,” Britton said. They worked with a company to develop microarray materials that could stand up to hydrogen sulfide.

Eventually they worked out many of the kinks and the “mini guts” enabled the researchers to conduct the C. difficile research. “The take-home message for my lab was: don’t get discouraged when things don’t go well right away,” Britton says.

While the Baylor laboratory first focused on C. difficile, the system could also be used to see how the microbiome responds to diet as well as to drugs and infections. Researchers might, for example, examine how the microbiome metabolizes parts of the diet into an active compound from an inactive one.

“There’s no limitation on using this,” Britton says. “You can develop a model that would be hard to recreate in an intact colon.”

Although the mini gut system offers a novel opportunity to study part of the microbiota in a microcosm, improvements will come with some more engineering solutions, Britton says.

He’s already thinking about next steps. These include trying to build an interface between the anaerobic bacteria and the aerobic human cells so that scientists can replicate long-term interactions between the host and microbiota. Scientists don’t completely understand how the interface between the aerobic cells and anaerobic bacteria works.

“Human cells need oxygen while the bacteria do not,” Britton says. “When you put them together, where does the oxygen go?”

It would be useful to look at bacteria that are attached to the gut lining as well as those in the liquid, so another step includes building a surface that could house mucus to mimic the human body, Britton says. It’s possible that engineers could use 3D printing technologies to test different designs.

Further engineering in these areas will eventually help build an even better mini gut to refine digestive tract medicines.

Melissa Lutz Blouin is an independent technical writer.