Cooperative Fish and Wildlife Research Units Program: Oregon
Education, Research and Technical Assistance for Managing Our Natural Resources

Oregon Project

Improving outcomes for hatchery-reared Chinook salmon through microbiome monitoring and enhancement

February 2022 - January 2024


Participating Agencies

  • Agricultural Research Foundation

Hatchery rearing and release programs have long been integral to salmon fisheries management as a way to supplement commercial and recreational harvests, and these programs have become increasingly important to fishers as wild stocks continue to decline. However, hatchery programs are also fraught with major challenges including poor hatchery fish performance. Improving the success of hatchery salmon and reducing the risks they present for wild populations could lead to greatly improved economic and ecological outcomes for Pacific salmon fisheries. This project directly addresses this management need by investigating the impacts of hatchery rearing on the microbial communities that populate the gastrointestinal (GI) tracts of Pacific salmon, specifically juvenile Chinook salmon. In salmonid species, the gut microbiome has shown potential as a useful tool for monitoring hatchery fish health and for reducing disease risk through probiotic enhancement. The goal of our research is to identify hatchery rearing practices that result in improved gut microbiomes for hatchery-reared juvenile salmon (i.e., gut microbiomes that are more likely to resemble those of wild fish). This information will inform hatchery management practices to improve disease resistance, enhance fitness, and potentially mitigate some of the negative effects of hatchery fish on wild populations by reducing disease transmission and competition. This work will be the first to address the causes and consequences of microbiome differences between hatchery and wild Pacific salmon and will lay the groundwork for future studies assessing the long-term effects of gut microbiome disruption on Pacific salmon populations.