Aquarium Microbiome Project
Shedd Aquarium’s first-of-its-kind laboratory looks all the way down to the microbial level to understand the basis of healthy aquarium ecosystems. By studying relationships between the countless unseen organisms in our environments and the animals in our care, our scientists are redefining our understanding of water quality, not just at Shedd but for aquariums everywhere.
Meet the Microbiome
Scientists now understand that controlling disease-causing microbes with antibiotics and super-hygienic practices can lead to the decline of vital beneficial microbes and the increasing prevalence of health problems in humans and wildlife alike. These include allergies and other inappropriate immune responses and even several behavioral disorders.
Aquariums are great places to study complex aquatic ecosystems. For every fish you meet at Shedd, there are 50 billion helpers you don’t see: microbes that filter the water, keep out opportunistic pathogens and help “train” the immune systems of resident animals.
Microbes are everywhere—on, in and all around every living thing, including fishes, dolphins and us—in communities called microbiomes. While some microbes cause disease, the majority are not only beneficial, they are also essential to the health and well-being of animals.
DNA sequencing technology allows us to take a microbial “census” to learn which organisms are present in our habitats and what their relative abundance is under different conditions. Samples might be habitat water from Stingray Touch or blowhole “snot” the dolphins have learned to project onto an overhead petri dish. They are analyzed in our microbiome laboratory, which opened in 2014. Shedd is the only U.S. aquarium with an on-site aquatic microbial-ecology lab.
For decades, the goal of the U.S. Department of Agriculture (USDA) water-quality standards set for aquariums was to minimize bacteria, whether they were good or bad. Now, Shedd’s scientists, in partnership with other researchers and the USDA, are engaged in a project that takes a new view of what constitutes a clean and healthy aquarium environment.
Shedd’s discoveries have enabled the animal care and animal health teams to fine-tune water-quality parameters to support beneficial microbiomes for the fishes, marine mammals and other animals. The results are also revolutionizing how the zoological profession manages environmental conditions for the optimal health of the animals in its care.
Applications extend to wildlife as well, from better diagnosing and treating stranded marine mammals to head-starting hatchling endangered turtles in an immunity-building microbial environment.
Related projects and staff
Using Microbes to Help Save Endangered Turtles
A conservation team-up has helped endangered western pond turtles rebound in Washington state, but the species’ recovery is threatened by a new fungal disease—one we’re trying to crack at the microbial level.
Dr. Bill Van Bonn
Dr. Bill Van Bonn oversees veterinary care for Shedd’s animals, emphasizing preventive care, cutting-edge techniques and state-of-the-art equipment.
Water-quality expert Allen LaPointe is responsible for replicating the native environmental conditions for each animal at Shedd.
Argonne National Laboratories
University of Illinois
University of Chicago
Illinois Institute of Technology U.S. Department of Agriculture.
The Shedd Aquarium Microbiome Project is made possible by generous gifts from aquarium supporters including the Institute of Museum and Library Services, National Science Foundation and Arthur and Elaine V. Johnson Foundation.