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  • Incorporating Gastrointestinal Microbiome Analysis into Fish Nutritional Assessments


Northwest Fisheries Science Center (NWFSC) Environmental and Fisheries Sciences


Sablefish GI microbiome
Incorporating Gastrointestinal Microbiome Analysis into Fish Nutritional Assessments
Sustainable culture of sablefish (Anoplopoma fimbria) is an active research area at NWFSC, with a primary objective of rearing a human food source under healthy, economic, and sustainable conditions. Development of sustainable feed for juvenile fish through replacement of marine fish oils is key for economic and ecological viability of sablefish culture.

This project intends to analyze the GI microbiome of juvenile sablefish, comparing three feeds (corn oil, linseed oil, BioOregon BioBrood) used in a National Marine Aquaculture Initiative (NMAI)-funded project examining the effects of substitute lipids on growth, production composition, and lipid bioconversion. Community DNA from GI mucus and luminal contents will be extracted, quantified, and quality checked. DNA will be submitted for analysis by a microbial phylogenetic microarray bearing over a million probes for classifying more than 59,000 bacterial taxa. Second Genome, a company with exclusive licensing for this phylogenetic microarray, will conduct the the analysis for classification, relative abundance, & ordination. Complementary to microbiome analysis, morphological changes in gastrointestinal tissues will be assessed for each fish by light microscopic histology (collaboration with Mark Myers). Although this is a stand-alone project, the objective is for the microbiome approach to become an integral component of finfish nutrition research.

Research Themes

Recovery and rebuilding of marine and coastal species
The Pacific Northwest is home to several iconic endangered species, including Pacific salmon and killer whales, and several rockfish species. Mandates such as the Endangered Species Act, MagnusonStevens Act, and the Marine Mammal Protection Act, grant NOAA Fisheries the authority to manage the recovery of depleted species and stocks. The NWFSC contributes to species recovery through research, monitoring and analysis, providing NOAA managers and regional stakeholders the tools and information they need to craft effective regulations and develop sustainable plans for recovery.

Research Foci

Evaluate the effects of artificial propagation on recovery, rebuilding and sustainability of marine and anadromous species
Artificial propagation has the potential to provide benefits both to species recovery and to seafood sustainability. Artificial propagation also poses risks to wild species and ecosystems. In the past, the use of artificial propagation has been an important risk factor for several threatened and endangered species, particularly Pacific salmon. Assessing the effects of artificial propagation is complicated by the fact that programs vary widely in size, rearing practices, and goals. The NWFSC conducts critical research on the influence of artificial propagation on population dynamics, growth rate, ecology of infectious disease, and the evolutionary fitness of wild fish and other marine organisms. Results of this research are needed to support the recovery of fish populations and have been especially valuable in providing critical information for recent, larger scale habitat restoration activities such as the Elwha Dam removal. NWFSC will continue to conduct science that informs the discussion about whether to allow fish to recolonize naturally after barrier removal, or to supplement populations with hatchery fish and on the impacts of aquaculture on fishing pressure and practices, and on the surrounding environment and ecosystem.


Alternative feeds
Use of non-marine protein for aquaculture feeds
The culture of fish, aquatic invertibrates, and aquatic plants for the production of food
fish diet
diet of fish
Microbial community & its interactions with a particular environment
common name for Anoplopoma fimbria. Other common names include black cod and butterfish.


Dietary effects on sablefish gastrointestinal microbiome & histology
Peer reviewed publication
Microbiome of Sablefish under Different Dietary Regimens
Aquaculture meeting presentation
Report to NOAA Aquaculture Program
Funding report


Class Actinopterygii
ray-finned fishes
Family Anoplopomatidae
Genus Anoplopoma
Kingdom Animalia
Kingdom Archaea
Kingdom Bacteria
Phylum Chordata
Phylum Euryarchaeota
Species Anoplopoma fimbria


Linda Rhodes
Principal Investigator
Maryjean Willis
Ronald Johnson
Internal Collaborator