Genome-wide insights into whole gut microbiota of rainbow trout, Oncorhynchus mykiss associated with changes in dietary composition and temperature regimens

Authors: IDENYI, J. - West Virginia State University; EYA, J. - West Virginia State University; ABANIKANNDA, M. - West Virginia State University; HUBER, D. - West Virginia State University; GANNAM, A. - Us Fish And Wildlife Service; Sealey, Wendy

Submitted to: Journal of the World Aquaculture Society
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/28/2023
Publication Date: 10/16/2023
Citation: Idenyi, J.N., Eya, J.C., Abanikannda, M., Huber, D.H., Gannam, A., Sealey, W.M. 2023. Genome-wide insights into whole gut microbiota of rainbow trout, Oncorhynchus mykiss associated with changes in dietary composition and temperature regimens. Journal of the World Aquaculture Society. 55(2):13028. https://doi.org/10.1111/jwas.13028.
DOI: https://doi.org/10.1111/jwas.13028

Interpretive Summary: Gut microbiomes play a significant role in the growth, metabolism, and health of fish. However, we know very little about interactive effects of variations of dietary composition and temperature on rainbow trout gut microbiota. These interactions have substantial implications for trout production efficiency as commercial diets continue to shift to include more plant-based ingredients and trout culture water temperatures rise with climatic changes. To investigate these effects, USDA ARS physiologist collaborated with researchers at West Virginia State University to conduct a comprehensive genome-wide examination of the the whole gut microbiota of rainbow trout fed different plant-based oil and protein sources and cultured at different water temperatures. These results will advance and improve aquaculture practices through enabling the development of sustainable and efficient diets that support fish growth and productivity while minimizing marine resource use.

Technical Abstract: Gut microbiota impacts fish metabolism, nutrient utilization, and health. However, we know very little about interactive effects of variations of dietary composition and temperature on rainbow trout gut microbiota. A total of 288 fish (average body weight:45.6g) were fed four iso-caloric, -lipidic, and -nitrogenous diets comprised 40% crude protein and 20% lipid and formulated as 100 % animal-based protein (AP) and blend of 50 fish oil (FO)/50 camelina oil (CO), 100 % AP and100 % CO, 100 % plant-based protein (PP) and blend of 50 FO/50 CO or 100 % PP and 100 % CO at 14 or 18°C water temperature. Gut content was analyzed using 16S rRNA gene and shotgun sequencing. Alpha-diversity did not change significantly. Regardless of diet, the dominant phyla were Tenericutes, Firmicutes, Proteobacteria, Spirochaetes, Bacteroidetes, and Actinobacteria. At the family level, Aeromonadaceae and Enterobacteriaceae dominated at 18°C, while Mycoplasmataceae dominated at 14°C. Moreover, gut microbes were dominated by genes relating to amino acid, carbohydrate, fat, and energy metabolisms and fatty biosynthesis significantly increased at 18°C. The functional profiles of the gut microbiota did not vary significantly among diets, except for a higher methionine and cysteine metabolism in fish fed plant ingredient compared animal diet, which suggests rainbow trout fed plant-derived protein mixed with CO could be as effective as those fed fish meals mixed with 50/50 FO and CO.