Shedd Aquarium Microbiome Project

The Shedd Aquarium Microbiome Project is the world’s first comprehensive look at microbiomes in a controlled aquarium ecosystem and how they influence animal health. Shedd Aquarium along with Argonne National Laboratory, the University of Illinois, Illinois Institute of Technology and the United States Department of Agriculture started this project to explore the unique relationships between the countless unseen living organisms that share our exhibit environments with the animals that live there. 

What is a microbiome?
Millions of microbes— bacteria, viruses and fungi — live in Shedd’s water habitats. Together, they make up tiny living communities or microbiomes. The majority of these microbes are not only beneficial, they are also essential to the health and well-being of the animals.

Why are microbiomes important?
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, other inappropriate immune responses and even several behavioral disorders.

Why study aquarium microbiomes?
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. Aquariums are also great places to study complex aquatic ecosystems. Closed habitats, with inputs, outputs and processes that are measured and documented with years of high-confidence data, enable us to explore how changes in environmental parameters have system-wide effects. Advances in DNA sequencing technology allow us to take a microbial “census” and know which organisms dominate our habitats under different conditions. The results of the studies conducted through the Shedd Aquarium Microbiome Project will revolutionize how we think about water quality and how we manage the environmental conditions in the exhibits for the optimal health of the animals.

Principal investigators for the Project are Dr. Bill Van Bonn, vice president for animal health and head of the A. Watson Armour III Center for Animal Health and Welfare, and Allen La Pointe, vice president overseeing environmental quality.


The Shedd Aquarium Microbiome Project is made possible in part by the generosity of The Grainger Foundation.

The Grainger Foundation