Germ-free transparent fish open new window into gut development

New model may help researchers understand and treat human digestive problems

Every animal — including humans — is home to “friendly” gut bacteria that help digest food and perform other important functions. Now, a tiny, transparent fish is literally offering biologists a new window into these mutually beneficial symbiotic relationships.
Researchers at Washington University School of Medicine in St Louis have shown for the first time that zebrafish can be raised in a germ-free environment. Zebrafish are transparent until they reach adulthood. Thus, these fish are providing researchers with unique opportunities to watch the gut develop with and without the beneficial effects of symbiotic bacteria.

“To untangle the complex interactions between humans and their friendly gut bacteria, we need simple animal models that can function as living test tubes,” explains principal investigator Jeffrey I. Gordon, M.D. “These models are key to identifying the genes and chemicals that allow friendly bacteria to enhance our health.”

Gordon is the Dr. Robert J. Glaser Distinguished University Professor and head of the Department of Molecular Biology and Pharmacology. The first author is John F. Rawls, Ph.D., a postdoctoral fellow in Gordon’s laboratory. The study, which will be published online the week of March 15 in the Proceedings of the National Academy of Sciences, also is the first to describe which bacteria normally reside in the zebrafish gut.

“Thanks to John’s painstaking work, we now have a new model for studying the molecular details of how symbionts affect animal development and physiology,” Gordon says.

Germ-free zebrafish arrive 50 years after scientists announced a similar biological feat: a viable strain of mice with no bacteria in their bodies. Gordon’s team believes zebrafish provide a nice complement to ongoing mouse research for several reasons. First, the zebrafish gut is organized in ways similar to the mammalian gut, and an international effort to sequence the zebrafish genome is almost complete. Zebrafish also are small — less than one centimeter long during development — so it is easy to raise large numbers at once. And finally, unlike mice, it is possible to watch the gut develop and function in transparent zebrafish.

After months of trial and error with different experimental conditions, the team finally succeeded in developing germ-free zebrafish that survived until late juvenile stages.

They discovered that several biological processes were disturbed in germ-free zebrafish. These impairments were similar to those the team had documented previously in germ-free mice. For example, the ability to process nutrients was compromised, as was the zebrafish’s immune system. Also, the cells that line the intestine were not renewed as rapidly. Because the lining of the gut is continuously exposed to potentially toxic substances, this process of renewing the gut lining is critical for maintaining health.

To begin to decipher the mechanisms underlying the observed abnormalities, the team determined the genetic profile of three groups of fish: a group raised under conventional conditions with bacteria; a group raised in a germ-free environment; and an initially germ-free group later colonized with normal gut bacteria. The comparison revealed 212 genes with different levels of expression in germ-free fish compared to the other two groups that had been exposed to bacteria. The researchers found 66 zebrafish genes that are analogous to genes regulated by friendly bacteria in the mouse intestine.

The team then began compiling a list of the bacterial species that reside in the zebrafish gut, which also has never been done before.

“We wanted to determine which constituents of the microbial community might be responsible for specific biological processes,” Rawls says. “To do that, you have to know something about the citizens in the bacterial community, which we didn’t. Using a molecular approach, we were able to identify a large number of types of bacteria that exist within the zebrafish digestive tract.”

With this list of microbial residents in hand, the team then could systematically recolonize germ-free animals with selected microorganisms. Using representatives from each of two major classes of organisms found within the zebrafish gut, they determined that some host responses are quite specific for a given type of bacteria while others are more general.

“The power of using germ-free animals is that you can define how a single species, or combinations of bacterial species, function to help complete animal development and to benefit adult physiology,” Gordon explains.

The team plans to use their germ-free zebrafish to characterize the chemicals produced by gut bacteria. According to Gordon, the chemical messengers developed by symbiotic gut bacteria over the course of millions of years of evolution could provide new approaches for supporting and healing the digestive system.

Rawls JF, Samuel BS, Gordon JI. Gnotobiotic zebrafish reveal evolutionarily conserved responses to the gut microbiota. Proceedings of the National Academy of Sciences, the week of March 15 2004.

Funding from the Ellison Medical Foundation and the National Institutes of Health supported this research.