Microbiome Research

The Shedd Aquarium Microbiome Project identifies actions we can take to support a beneficial microbiome for the animals in our care. Our research advances our knowledge of the impact of management practices on microbial communities and adds to a growing understanding of their importance for animal and environmental health. 

Our research interests include

  • Impact of disinfection practices on microbial assemblages and resident fitness in regulated marine mammal systems
  • Mechanisms of selection for pathogenic Mycobacterium species in fish systems
  • Impact of disinfection practices and antimicrobial treatment on nitrification processes essential to aquarium management

The project is headquartered at a dedicated microbial ecology laboratory within the aquarium. On-site capabilities include automated DNA purification, quantitative PCR and high-throughput 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.

Recent studies completed

  • Impact of water re-use on microbial diversity in the 3-million-gallon Abbott Oceanarium (Kent et al., in preparation)
  • Virome characterization of water samples from six Shedd exhibits (Kim et al., Frontiers in Microbiology, 2017)
  • Shifts in microbial ecology of a cold marine fish system pre- and post-90 percent water change (Van Bonn et al, Zoo Biology, 2015)
  • Influence of native, transport, quarantine and exhibit environments on skin-associated microbiota of cricket frogs and spring peepers
  • Microbial networks in Abbott Oceanarium and impact of probiotic administration in dolphins (Cardona et al., in review, Microbiome)
  • Evaluation of standard methods for identifying PseudomonasEnterococcus and Staphylococcus species in marine mammal pool waters
  • Coliform counts and their relationship to bacterial and archaeal communities in a sea lion reserve system
  • Microbiome comparison of artificial marine mammal habitat water across five AZA-accredited facilities
  • Air microbiome and fungal pathogen surveillance during routine exhibit maintenance
  • DNA sequencing and analysis for the comparison of gut microbiota between differentially managed populations of two endangered species: pygmy rabbits (with Washington Department of Fish and Wildlife) and Bahamian rock iguanas (with Chuck Knapp, Conservation Research Team, and Utah State University)

Ongoing studies


  • Role of environmental microbiome in artificial rearing environments of the endangered western pond turtle, an AZA S.A.F.E. (Saving Animals From Extinction) priority species
  • Gut microbial diversity of malnourished California sea lion pups (with the Marine Mammal Center, a rescue and rehabilitation facility in Sausalito, CA)
  • Source tracking of microorganisms in pre-exhibit water through intake, carbon filtration, reverse osmosis, salination and storage
  • Microbiome comparison of Amazon Rising and South American river habitats across institutions
  • Impact of probiotic treatment on host-associated microbiome and immune response of cetaceans
  • DNA sequencing and analysis for: genotyping of Bahamian conch in and around a marine protected area (with Andy Kough, Shedd Conservation Research team)
  • More to come!


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

The Grainger Foundation