First Advisor

Kim H. Brown

Date of Publication

Spring 7-10-2017

Document Type


Degree Name

Master of Science (M.S.) in Biology






Gastrointestinal system -- Microbiology, Salmonidae -- Habitat -- Pacific Northwest, Steelhead (Fish), Rainbow trout, Salmon fisheries, Lipids -- Metabolism



Physical Description

1 online resource (vii, 108 pages)


The Pacific Northwest is known for its once-abundant wild salmonid populations that have been in decline for more than 50 years due to habitat destruction and commercial overexploitation. To compensate, federal and state agencies annually release hundreds of thousands of hatchery-reared fish into the wild. However, accumulating data indicate that hatchery fish have lower fitness in natural environments, and that hatchery rearing negatively influences return rates of anadromous salmonids. Recently, mounting evidence revealed that the richness and diversity of intestinal microbial species influence host health. We examined the gut microbiota of pre-migratory hatchery-reared steelhead (Oncorhynchus mykiss) to assess microbial community diversity. The Cascade Mountains serve as an allopatric border between two distinct clades of steelhead that show significant differences in genomic and mitochondrial diversity. We identified differences in core microbiota of hatchery-reared fish that correlate with this divergent phylogeographic distribution. Steelhead sampled from hatcheries east of the Cascades had overall greater core gut microbiota diversity. These differences were found despite similarities in diet and rearing conditions.

In addition to taxonomic variation across the geographic divide, we identified significant differences in metabolic pathways using PICRUSt gene prediction software. Our analysis revealed significant enrichment of genes associated with lipid metabolism in the gut microbiome of western fish. 8 of 19 individual lipid metabolism pathways were more prominent in western populations. Lipids are a vital nutritional component for teleost species involved in migration and subsequent return for spawning in natal environments. We hypothesize that the observed differences in lipid metabolism across this phylogenetic divide results from an increased ability of eastern Cascade (O. m. gairdneri) fish to utilize lipids taken in via the diet. This increased absorption and utilization would make lipids less available for the intestinal microbiota of the eastern fish, as evidenced by the lower abundance of lipid metabolism genes in the east. Our research utilizes information from the microbiome to understand the phenotypic implications occurring in segregated populations of hatchery-reared steelhead, further confirming elements of coevolution between an organism and its internal environment.


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All supplemental files located in the Additional Files below are Excel documents and must be opened through the Excel Program

Persistent Identifier

3432_total_OTUs.xml (10613 kB)
Supplemental 1.

all_taxa_phylum.xml (116 kB)
Supplemental 2.

all_taxa_class.xml (265 kB)
Supplemental 3.

all_taxa_order.xml (482 kB)
Supplemental 4.

all_taxa_family.xml (932 kB)
Supplemental 5.

all_taxa_genus.xml (1757 kB)
Supplemental 6.

all_taxa_species.xml (2062 kB)
Supplemental 7.

core_microbiota_east.xml (38 kB)
Supplemental 8.

core_microbiota_west.xml (13 kB)
Supplemental 9.