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Shedd Research Under the Microscope: The Aquarium Microbiome Project

For every animal at Shedd, there are billions of microbes you can’t see. They help filter water and help develop the immune systems of resident animals. As laboratory manager for the Shedd Aquarium Microbiome Project, Frank Oliaro’s job is to study these tiny helpers.

Multitudes of microbes— bacteria, viruses and fungi — live in Shedd’s water habitats as well as on our own bodies. Together, they make up tiny living communities or microbiomes. Most of these microbes are not only beneficial, some are also essential to the health and well-being of animals and people. Microbiome research is a rapidly growing field with critical applications in health, science and hygiene.

A dolphin looks on as a water sample is taken from the habitat for Shedd's Microbiome Project.

Multitudes of microbes— bacteria, viruses and fungi — live in Shedd’s water habitats as well as on our own bodies. Together, they make up tiny living communities or microbiomes. Most of these microbes are not only beneficial, some are also essential to the health and well-being of animals and people. Microbiome research is a rapidly growing field with critical applications in health, science and hygiene.

From shows like Brooklyn Nine-Nine to body wash ads and special diets to promote gut health, microbiomes have become trendy, and Frank agrees. In addition to general popularity, he describes it as a “fad” for its surface level of understanding. Research into microbiomes is exploding with new scientific papers published every day. Despite its growth, however, much in the conversation of microbiomes in mainstream media is based on nothing. “I don’t think there is a ton of research yet, or enough data to back up a lot of the claims people are making right now,” Frank says. He is confident that, with the progress in the field currently, there will be concrete answers in the future.

“Shedd is a really forward-thinking place,” Frank says. At the time that the Shedd Aquarium Microbiome Project launched, in 2014, microbiome research was a new field that primarily addressed human health. But the aquarium’s animal health team, administrators and board members saw its potential for raising the bar in animal care and committed to building a research team and a state-of-the-art laboratory space to house it.

Lab manager Frank Olario, wearing safety googles, rubber gloves and a lab coat, lifts a petri dish out of a large centrifuge in Shedd's microbiome lab.
A microscope slide showing stringy clumps of round purple bacteria.

The Aquarium Microbiome Project is the world’s first comprehensive look at aquatic microbiomes in a controlled aquarium ecosystem and how they influence animal health. Yet similarities exist between the research done in hospitals and universities and that done in an aquarium: Both humans and the animals at Shedd live in “built environments.”

A lot of microbiome research delves into the built environment of humans—for example, what are the microbes on a cell phone and how do they get transported elsewhere? This is called a network analysis of a microbiome, and it’s popular within the research community. Similarly, it is important for Shedd to understand how microbiomes develop in the built environment of an aquarium, where the goal is to stay true to the natural environment. For example, it was previously believed that the fewer bacteria present in exhibit water, the better it was for the animals. Yet microbiome research reveals that totally sanitized environments may put animals at a greater risk for infection and disease. Today, we embrace the natural microbial diversity necessary to keep Shedd’s animals healthy and safe.

When the Microbiome Project began, the team outlined a series of goals with a science advisory committee of renowned microbial specialists. One of the goals is to determine the optimal degree of disinfection in marine mammal habitat water. Shedd must comply daily with water-quality standards set by the U.S. Department of Agriculture specifically for zoological organizations. The regulations have historically encouraged keeping bacteria counts low. Shedd is gathering data on how these regulations actually affect the health of the animals. This work could ultimately affect the aquarium profession as a whole, potentially changing regulations that were implemented in an era before microbiome research was possible.

What we are learning in our microbiome lab also has applications beyond our habitats.

A western pond turtle is held by its shell by a Shedd researcher in Oregon State.

In Washington state, western pond turtle numbers had plummeted to unsustainable levels. The Washington Department of Fish and Wildlife, Seattle’s Woodland Park Zoo and Oregon Zoo launched an extensive, long-term recovery effort to save this state-endangered reptile and prevent the extinction of Washington populations. The project is ongoing.

To increase survivorship of hatchlings, which are on many non-native predators’ menus, they began collecting eggs from wild nests, hatching them in incubators and raising the baby turtles to a sturdy, more predator-proof size before returning them to the wild. This process, called head starting, has been successful with many endangered wildlife species, and the Washington western pond turtle populations grew slowly but steadily. But a shell disease began appearing among the released turtles, and it might affect the overall recovery of this species.

Shedd’s Microbiome Project team was invited to Washington to help figure out what was causing the shell disease, which appears to be more prevalent in turtles that have spent time in human care, including head-started individuals. Studies are underway to examine the microbial diversity of the environments where these turtles are reared. Efforts are being made to determine what changes could be implemented to enhance the microbial diversity, thereby potentially bolstering the young turtles against the shell disease. Now we understand that the places these turtles were brought up will ultimately impact them later in life.

(The western pond turtle is a focus species of the Association of Zoos and Aquarium’s Saving Animals From Extinction [SAFE] initiative. The western pond turtle recovery effort by Woodland Park Zoo and Oregon Zoo, assisted by Shedd, is part of this program.)

Today microbiome awareness permeates all facets of science—as well as popular culture—in a rapidly expanding field of research. “Questions come about and then ideas are generated. Then there’s an explosion of study in a field,” Frank says about the progress of science. The future of science will no doubt be filled with more answers and even more questions, but, Frank says, “right now we’re in that explosion of the microbiome research field.” Our microbiome team is contributing with innovative research and accompanying scientific papers that promise to keep Shedd at the leading edge of this rapidly evolving science.