Commensal organisms are an integral part of all vertebrates, contributing heavily to development, pathogen defense, and metabolism. Commensals reside at different body sites within vertebrate animals creating unique and distinct communities that vary between locations. The human microbiome project has revealed distinct bacterial community compositions at the diverse range of body sites that have been sampled, providing evidence for different functional purposes of each microbiome. Rainbow trout, Oncorhynchus mykiss, serves as a model organism for the study of mucosal physiology and immunology. Teleost fish are evolutionarily important as one of the first jawed vertebrates with a dedicated adaptive mucosal immune system, as well as being vital to aquaculture practices. Studies of the microbiome of rainbow trout have the potential to 1) reveal important mucosal evolutionary processes 2) discover particular symbtiotic bacteria that can be used in aquaculture to improve fish health. The hypothesis of the present study is that different body sites of rainbow trout possess distinct commensal bacterial communities. Using 454 pyrosequencing of the 16S bacterial rRNA, we present the first topographical map of the microbiome of rainbow trout. Body site is a strong predictor of bacterial community composition in trout. Both ANOSIM and Adonis statistical analysis revealed p values below 0.001 when using body site as a variable to describe diversity. The most diverse mucosal sites are the skin and the olfactory organ with 17 and 18 different phyla, respectively. We also discovered a novel and high diversity of bacteria present within the skin epithelium of rainbow trout, dominated by Propionibacterium sp. and Staphyloccus sp. This may represent a unique adaptation in salmonids to avoid swimming drag forces that bacteria attached to the external mucus may cause.
microbiome, teleosts, rainbow trout, skin epithelium, antifungal properties
Level of Degree
UNM Biology Department
First Committee Member (Chair)
Second Committee Member
Lowrey, Liam T.. "The microbiome of rainbow trout (Oncorhynchus mykiss)." (2014). https://digitalrepository.unm.edu/biol_etds/73