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

Hatchery rearing and release programs have long been integral to Pacific salmon fisheries management, helping to supplement commercial and recreational harvests as wild stocks decline; however, these programs have faced significant challenges, including poor performance of hatchery-reared salmon. Addressing these challenges is critical for achieving improved economic and ecological outcomes for Pacific salmon fisheries. This project tackled a key aspect of this issue by investigating how hatchery rearing practices impact microbial communities in the gastrointestinal (GI) tracts of juvenile Chinook salmon, specifically focusing on the gut microbiome’s role in fish health and disease resistance. 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 this research was to identify hatchery rearing practices that resulted in improved gut microbiomes for hatchery-reared juvenile salmon (i.e., gut microbiomes that were more likely to resemble those of wild fish). Through collaboration with pathologists and microbiologists at Oregon State University, this study was one of the first to directly address the causes and consequences of microbiome differences between hatchery and wild salmon and to link these differences to potential disease resistance. The results will inform hatchery management practices that enhance disease resistance and ecological compatibility, supporting healthier fisheries and laying the foundation for further studies on the long-term effects of microbiome disruption in Pacific salmon populations.