Aquaculture provides sustainable production of food fish with high protein/low-saturated fat to satisfy increasing demand. Globally, efficient and environmentally sustainable aquaculture production systems are urgently required. Over two decades of selective breeding, our research resulted in development of a rainbow trout strain that grows as well on an all-plant (about 50% soy based products) protein diet as on a fishmeal-based diet, and grows much faster than non-selected trout. In aquaculture, infectious diseases are the primary cause of economic losses, leading to the loss of millions of pounds of cultured product. Disease outbreaks are recognized as a significant constraint on aquaculture production, affecting its economic development. Disease susceptibility in fish is affected by intrinsic (genetic) and extrinsic (water quality, rearing density, feed rate, diet) factors and their interactions. The aquatic environment harbors a complex and dynamic microbial community (microbiota) and is in continuous contact with fish. In addition to selection for growth on replacement diets, families are tested for resistance to infectious hematopoietic necrosis virus (IHNV) and Flavobacterium spp. Each year, controls and crosses are also generated utilizing fish from the selected lines and from non-selected control lines to verify differences related to dietary tolerance and utilization. The ARS/UI fish are likewise being raised commercially under large scale production and evaluations are taking place that compare the survival of our selected fish to other strains under production conditions. Currently, we are using 53% soy protein (35% SBM and 18% SPC) for our selected plant diet for ARS/UI fish (trout). However, we would like to optimize the SBM and SPC level in the diet of selected (ARS/UI) trout and commercial trout by considering growth, gut health and resistance against viral and bacterial disease. Overall, successful completion of this project will have a broad application to commercial fish selective breeding programs, leading to increased profitability for US soy producers and fish farmers. The overall goal for this research project then is to determine the molecular mechanisms behind enhanced non-specific resistance in rainbow trout, while also studying the underlying innate immune changes that occur through disease selection. Again, the price of feed and losses to disease are the highest production costs and, therefore, the ability to reliably convey elevated, persistent non-specific immunity to other strains and/or species would be of great advantage for all aquaculture producers.

The overall goal of our proposed project is threefold: i) increase the usage of soybean meal (SBM) and decrease the soy protein concentrate in feeds for the commercial production of Rainbow trout; and ii) demonstrate how
selected trout for soy-based diet can improve their resistance against pathogen; and iii) overall soybean-based feed can improve profits for fish farmers. For this project, we will work toward improving our understanding of
fish-disease dynamics, with the long-term goal of reducing losses to the U.S. rainbow trout industry. For this one year period, we will address this goal with the following objectives:
Objective #1: Define the best feed formulation to incorporate maximum amount of soybean meal (SBM) and decrease the soy protein concentrate (SPC) in two lines (selected and commercial) of rainbow trout diet
Objective #2: Optimize the SBM inclusion level in trout by measuring growth performance, feed utilization, intestinal barrier function, immune related parameters and gut microbiome
Objective #3: Determine the effects of pathogens (viral pathogen, Infectious hematopoietic necrosis virus, IHNV and bacterial pathogen, Flavobacterium psychrophilum, Fp) challenge on survival, immunomodulation, and gut
health in rainbow trout.
Objective #4: To examine and genes expression, distal intestinal structure (enteritis), intestinal barrier function
and gut microbiome in pre and post challenge study of trout strains with different genetic backgrounds.

This project will increase the socio-economic condition of fish farmers and the aqua feed industry, by producing fish at low cost using soybean diet, which can reduce the U.S. trade deficit, and mitigating the strain on natural
marine fish for fishmeal. This is a great news for soy producers as demand of soy protein will be increased in aquafeed. Fish farmers will be interested to adopt the low-cost alternative method to select the fish families to utilize the soy based diets. At the completion of the project genetic selection should improve the soy meal utilization which means soybean consumption will greatly increase simultaneously in aquafeed industry.

Updated June 20, 2024:
Goal and Objectives:
The overall goal of our proposed project is threefold: i) increase the usage of soybean meal (SBM) and decrease the soy protein concentrate in feeds for the commercial production of Rainbow trout; and ii) demonstrate how selected trout for soy-based diet can improve their resistance against pathogen; and iii) overall soybean-based feed can improve profits for fish farmers. For this project, we will work toward improving our understanding of fish-disease dynamics, with the long-term goal of reducing losses to the U.S. rainbow trout industry. For this one year period, we will address this goal with the following objectives:

Objective #1: Define the best feed formulation to incorporate maximum amount of soybean meal (SBM) and decrease the soy protein concentrate (SPC) in two lines (selected and commercial) of rainbow trout diet.
Objective #2: Optimize the SBM inclusion level in trout by measuring growth performance, feed utilization, intestinal barrier function, immune related parameters and gut microbiome
Objective #3: Determine the effects of pathogens (viral pathogen, Infectious hematopoietic necrosis virus, IHNV and bacterial pathogen, Flavobacterium psychrophilum, Fp) challenge on survival, immunomodulation, and gut health in rainbow trout.
Objective #4: To examine and genes expression, distal intestinal structure (enteritis), intestinal barrier function and gut microbiome in pre and post challenge study of trout strains with different genetic backgrounds.

Fish Growth and Disease Trials:

Feed ingredients and diet formulation: Based on our previous work, soybean meal-based diets (SBM diet) have been formulated to contain 43% crude protein and 22% crude lipid. All five diets are isonitrogenous and isolipidic. All five-diet formulations were designed to meet the essential amino acid (EAA) requirements of juvenile Rainbow trout.

Five experimental diets:
Diet 1: Control feed - 0% SBM/SPC + 30% fishmeal (FM)
Diet 2: 13% SBM + 20% SPC
Diet 3: 23% SBM + 13% SPC
Diet 4: 34% SBM + 7% SPC
Diet 5: 45% SBM + 0% SPC

Feed Extrusion: Feeds have been manufactured at USDA, Bozeman Fish Technology Center, Bozeman, MT and were shipped to ARI, University of Idaho, Moscow ID.

Experimental setup: Rainbow trout eggs were acquired from two commercial sources, ARS/UI and Trout Lodge, hatched and reared to ~5 grams. The growth trial will begin late June 2024 and will be followed by the disease challenge trials.

Updated March 28, 2025:
Goal and Objectives:
The overall goal of our proposed project is threefold: i) increase the usage of soybean meal (SBM) and decrease the soy protein concentrate in feeds for the commercial production of Rainbow trout; and ii) demonstrate how selected trout for soy-based diet can improve their resistance against pathogen; and iii) overall soybean-based feed can improve profits for fish farmers. For this project, we will work toward improving our understanding of fish-disease dynamics, with the long-term goal of reducing losses to the U.S. rainbow trout industry. For this one year period, we will address this goal with the following objectives:

Objective #1: Define the best feed formulation to incorporate maximum amount of soybean meal (SBM) and decrease the soy protein concentrate (SPC) in two lines (selected and commercial) of rainbow trout diet.
Objective #2: Optimize the SBM inclusion level in trout by measuring growth performance, feed utilization, intestinal barrier function, immune related parameters and gut microbiome
Objective #3: Determine the effects of pathogens (viral pathogen, Infectious hematopoietic necrosis virus, IHNV and bacterial pathogen, Flavobacterium psychrophilum, Fp) challenge on survival, immunomodulation, and gut health in rainbow trout.
Objective #4: To examine and genes expression, distal intestinal structure (enteritis), intestinal barrier function and gut microbiome in pre and post challenge study of trout strains with different genetic backgrounds.

Fish Growth and Disease Trials:

Feed ingredients and diet formulation: Based on our previous work, soybean meal-based diets (SBM diet) were formulated to contain 43% crude protein and 22% crude lipid. All five diets are isonitrogenous and isolipidic. All five-diet formulations were designed to meet the essential amino acid (EAA) requirements of juvenile Rainbow trout.

Five experimental diets:
Diet 1: Control feed - 0% SBM/SPC + 30% fishmeal (FM)
Diet 2: 13% SBM + 20% SPC
Diet 3: 23% SBM + 13% SPC
Diet 4: 34% SBM + 7% SPC
Diet 5: 45% SBM + 0% SPC

Feeds were manufactured at USDA, Bozeman Fish Technology Center, Bozeman, MT and were shipped to ARI, University of Idaho, Moscow ID. Both the growth trial and the disease trial were completed, all analysis done, and data is included in the attached final report.

Growth Trial Conclusions:
This study highlights strain-specific responses to SBM-based diets in rainbow trout. While moderate SBM inclusion (up to 34% SBM, 6.5% SPC) maintained growth and feed efficiency, higher SBM levels (M45/C0) negatively impacted performance, likely due to anti-nutritional factors and gut stress. The commercial strain showed superior nutrient utilization and metabolic efficiency, whereas the Hagerman strain had higher feed intake but lower assimilation, requiring strain-specific diet adjustments. The Hagerman strain exhibited greater intestinal remodeling and immune activation, reflected in higher goblet cell density, connective tissue changes, and gut barrier gene expression. While moderate SBM levels did not impair gut health, excessive SBM induced mild gut stress, particularly in the Hagerman strain. At the hepatic level, higher immune and oxidative stress markers (S100V2, GPx) in the Hagerman strain suggest increased metabolic burden, while the commercial strain maintained stability. Overall, SBM inclusion up to 34% with relatively less SPC (6.5%) is a viable fishmeal alternative, but strain-specific formulations are necessary to optimize growth while minimizing gut and metabolic stress, particularly in the Hagerman strain.

Disease Trial Conclusions:
This challenge study suggests that strain-specific and pathogen-dependent immune strategies play an important role in disease resistance in rainbow trout. The Hagerman strain was significantly more susceptible to F. psychrophilum, with higher mortality, greater tissue necrosis, and reduced post-challenge autophagic activation, whereas the commercial strain exhibited stronger innate and inflammatory responses, as seen in both gene expression and histopathology. In contrast, under IHNV-challenge, differences between strains were less pronounced, although the Hagerman strain exhibited a more robust adaptive response, particularly in the head kidney. Although dietary treatments did not significantly affect survival, 34% SMB/6.5% SPC consistently enhanced immune gene expression and maintained a balanced inflammatory and autophagic response without causing excessive tissue damage. Compared to the FM control, SBM/SPC-based diets, particularly that with 34% SMB/6.5% SPC, showed a clear immunomodulatory benefit under pathogenic challenge. In contrast, 23% SBM/13% SPC was linked to increased inflammation and mortality, suggesting the importance of optimizing SBM/SPC ratios.

View uploaded report

Overall, successful completion of this project will have a broad application to commercial fish selective breeding programs, leading to increased profitability for US soy producers and fish farmers.