Microbiome Research

The primary goal of the Shedd Aquarium Microbiome Project is to identify actions we can take to support a beneficial microbiome for the animals in our care. A secondary aim is to provide evidence to inform how all types of aquatic systems are managed to optimize health.

Specific research interests include:

  • Impact of disinfection practices on the composition and diversity of microbial assemblages in regulated marine systems housing cetaceans
  • Mechanisms of selection for pathogenic Mycobacterium species in freshwater systems
  • Impact of disinfection practices and antimicrobial treatment on nitrification

The project is headquartered at a dedicated microbial ecology laboratory within the aquarium. Onsite capabilities include automated DNA extraction and next-generation sequencing on the Illumina MiSeq platform. 

If you’d like to know more about the work Shedd is doing or how to get involved, email the Microbiome team. More details about our studies can be found below.


  • Impact of water re-use on microbial diversity in the 3 million gallon Abbott Oceanarium
  • Characterization of a cold saltwater fish system pre- and post-90 percent water change (Van Bonn et al, Zoo Biology, 2015)
  • Surveillance of amphibian-associated microbiome at acquisition and through quarantine
  • Virome surveillance of diverse aquarium habitats including Stingray Touch and Sturgeon Touch exhibits (Michigan State University, Kim et al, submitted for publication)
  • High-resolution surveillance and source tracking of bacterial assemblages associated with cetaceans, habitat and handlers in Abbott Oceanarium (University of Chicago, in process, anticipated publication 2017)
  • Comparison of yellow stingray-associated microbiome between Shedd animals and Bahamian populations surveyed aboard the Coral Reef II
  • Evaluation of health and microbial ecology in cownose rays housed in different aquarium habitats (University of Illinois, Johnson et al, submitted for publication)


  • Effect of temperature cycling on the aquatic microbiome of sea otter and cetacean habitats
  • Air microbiome surveillance during routine maintenance and exhibit renovation
  • Comparison of artificial dolphin habitats across three AZA member institutions
  • Impact of UV disinfection and CO2 treatment on mycobacterial abundance and community structure in artificial freshwater systems


  • Impact of ozone treatment on water chemistry and microbial diversity in cetacean systems
  • Relationship between coliform counts and bacterial community structure in artificial seawater housing cetaceans
  • Culture-dependent studies of Pseudomonas, Enterococcus and Staphylococcus species under varying conditions of disinfection
  • Source tracking of microorganisms in pre-exhibit water through intake, carbon filtration, reverse osmosis, salination and storage
  • Amazon Rising exhibit characterization and comparison with like exhibits
  • Impact of probiotic treatment on host-associated microbiome and immune response of cetaceans
  • More to come!


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

The Grainger Foundation