Winding its way through southern Idaho, the Snake River sidles along a stretch of dark basalt rising above arid farmland. In the Thousand Springs region, an enormous aquifer sends water bursting from the rock in a cavalcade of waterfalls and creeks. Cold, clear, and full of oxygen, the water is heaven for rainbow trout, and life-giving to some of the world’s largest trout farms.
A few hundred miles to the north, water bubbles and roars through pipes at the University of Idaho Aquaculture Research Institute in Moscow. Researchers Kenneth Cain ’97 PhD and Douglas Call ’87 BS and ’97 PhD, gently net young rainbow trout from large round tanks and examine them for signs of coldwater disease.
Cain, professor and associate director of the institute, says that coldwater disease occurs in the wild but is most prevalent in commercial trout and salmon hatcheries, where crowding and stress lead to frequent outbreaks. The deadly bacterial infection eats away the trout’s skin, leaving ragged ulcers. The disease kills up to 30 percent of hatchery stock and causes millions of dollars in losses.
After 15 years of effort, Cain and Call have developed a simple and effective method to combat coldwater disease by turning some of the trout’s own intestinal bacteria into infection-fighting probiotics. They also showed that the probiotics work by secreting a toxic protein, which does not harm the fish but does kill the coldwater disease organism, Flavobacterium psychrophilum.
Call, a professor in the Paul G. Allen School for Global Animal Health at Washington State University, and his graduate student, Carla Schubiger ’15 PhD, reported the findings earlier this year in the journal Applied and Environmental Microbiology.
“Coldwater disease is the number one bacterial illness affecting U.S. trout aquaculture and to a lesser extent coho salmon,” says Call. “Once an outbreak starts, the only way we’ve had to treat it has been with antibiotics. The problem with antibiotics is that they can lead to bacterial resistance and also contaminate the water and soil.”
Call believes the probiotics could be an economical alternative to antibiotics, and welcome news to the global $13.7 billion salmonid aquaculture industry.
He retrieves a vial of dark brown pellets and pours some into his hand. “Fish food coated with the probiotic,” he explains. “The bacteria are fast growing, cheap to produce, and easy to feed to the fish—all the attributes of an ideal preventative treatment.”
The pellets are part of a new frontier in medicine—use of the body’s natural population of bacteria, called the microbiome, to boost health and immunity. The National Institutes of Health estimates that bacteria outnumber our body’s cells ten to one. While no one knows the full extent of the microbiome’s impact on human health, scientists do know the 370 trillion bacteria in each of our bodies are essential for life.
Livestock producers hoping to leverage the microbiome sometimes feed their animals probiotics like Lactobacillus to promote disease resistance and overall health. But Call says most products are unregulated and unproven. “It’s kind of the Wild West in terms of claims of what these things can do.”
Even more valuable is Schubiger’s remarkable discovery of the probiotic toxin, which confirms how the bacteria successfully fight the coldwater disease organism.
Many of her research hours were spent in the waters of the Snake River at Clear Springs Foods. Located in Buhl, Idaho, it is the largest trout farm in the world. During a winter snowstorm, Schubiger waded hip deep among thousands of trout as the scientists ran some early trials on the probiotic.
“It’s a unique setting with cold water trout farms on one side of the river and hot springs with tropical fish farms on the other side,” she recalls fondly. “It is an absolutely breathtaking and beautiful landscape.”
Schubiger became involved in the project after Cain painstakingly searched through intestinal bacteria from trout to identify possible probiotic candidates. Field trials confirmed that an Enterobacter species called C6-6 helped fish survive coldwater infection, but as is common with many probiotics, the scientists really didn’t know how it worked.
Call asked Schubiger if she’d like to try to pinpoint what makes C6-6 so effective. After some frustrating challenges, she determined the probiotic produces a toxic protein that inhibits the coldwater bacteria.
“It was surprising,” she says. “The protein had been overlooked and undervalued for 25 years. At first I was skeptical about putting all my effort into testing this one peptide—it was risky, but we were lucky and it panned out.”