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Item The influences of diet and water systems on rainbow trout gut microbiome in relation to nutrient utilization(Montana State University - Bozeman, College of Agriculture, 2017) Betiku, Omolola Comfort; Chairperson, Graduate Committee: Carl Yeoman; T. Gibson Gaylord and Wendy M. Sealey were co-authors of the article, 'Evaluation of protein reduction and essential amino acids supplementation of plant- and animal protein-based diets on production of rainbow trout (Oncorhynchus mykiss)' submitted to the journal 'Journal of the World Aquaculture Society' which is contained within this thesis.; Carl J. Yeoman, T. Gibson Gaylord, Suzanne L. Ishaq, Glenn C. Duff, Aurelien Mazurie and Wendy M. Sealey were co-authors of the article, 'Divided nutritive function of the rainbow trout (Oncorhynchus mykiss) mid- and hind- gut microbiomes' submitted to the journal 'Frontiers in microbiology' which is contained within this thesis.; Carl J. Yeoman, T. Gibson Gaylord, Glenn C. Duff, Brian Bothner, Stephanie S. Block and Wendy M. Sealey were co-authors of the article, 'Differences in amino acid catabolism by gut microbes with/without prebiotics inclusion in GDDY-based diet affect feed utilization in rainbow trout' submitted to the journal 'Aquaculture' which is contained within this thesis.; Carl J. Yeoman, T. Gibson Gaylord, Ben Americus, Sarah Olivo, Glenn C. Duff and Wendy M. Sealey were co-authors of the article, 'Water system is a controlling variable modulating bacterial diversity of gastrointestinal tract and performance in rainbow trout' submitted to the journal 'Plos one' which is contained within this thesis.Plant protein ingredients are sustainable sources of protein that could be used to meet the demand of the growing aquaculture industry. However, feeding plant protein diets has some drawbacks in terms of reduced growth and poor feed efficiency. This dissertation evaluated the production cost of alternative protein diets for commercial production of rainbow trout. Also, it identified the microbiota and gene functions associated with alternative diets and how they differ between mid- and hind-gut sections of the rainbow trout intestine. Furthermore, it determined differences in microbial community compositions and functions in the luminal and mucosal GIT of trout when fed alternative diets, with/without prebiotics. Lastly, the significance of diet and water as environmental factors shaping the mucosal and luminal bacterial compositions in trout was investigated. Experiment 1 demonstrated that trout growth and body indices were not affected by feeding plant protein diet (PPD). In experiment 2, shotgun metagenomics revealed predominant bacterial population in trout microbiota. Genes related to carbohydrate metabolism were increased in the hindgut intestine of those fed PPD. Experiment 3 demonstrated that replacing fishmeal with 75% GDDY did not alter growth of trout, but not feed intake and feed conversion ratio (FCR). High inclusion of GDDY in trout diet resulted in enrichment of catabolic genes involving branched chain amino acids in trout midgut region. Experiment 4 showed that rearing in a recirculating water system significantly improved trout performance compared to rearing in a flow-through water system, while feed intake and FCR increased in fish raised in the flow-through system. Water samples were more diverse than GIT samples. Bacterial diversity was greater in mucosal scrapings of the GIT than in the lumen. Water system played a major role influencing the microbial communities in trout luminal and mucosal GIT. The lumen shared similar bacteria with the rearing water. The results of this study demonstrated that plant protein can effectively substitute for fishmeal in trout diets. It further showed that trout GIT microbiota vary between the mid- and hind-GIT. The hind-, but not the mid-GIT microbiome appears to be modulated by diet, while the mid-GIT is affected by water system.Item Investigation of the effects of copper source, copper and zinc levels, and dietary protein source on CU bioavialability in rainbow trout(Montana State University - Bozeman, College of Agriculture, 2012) Read, Elizabeth Stevens; Chairperson, Graduate Committee: John Paterson.Limited research has examined the effects that plant-based diets have on copper (Cu) and Zinc (Zn) absorption and utilization in rainbow trout. Few studies have been conducted to determine if interactions exist in the utilization of Cu when increasing levels of supplementary Zn were offered. The objectives of this research were to: first determine what effect protein source (plant vs. animal based), Cu source (complex vs. inorganic) and concentrations of Cu (0, 5, 10, 15, 20 ppm) in the diet had on rate and efficiency of gain and Cu tissue levels in rainbow trout. The second experiment was to determine if interactions occur due to increasing diet content of Zn (0, 30, 300, 1500 ppm) and Cu provided at two levels (0 or 10 ppm) on tissue levels of Cu in rainbow trout. From experiment one, trout fed plant-based diet had higher (P < 0.05) ADG and improved (P < 0.05) FCR in comparison to fishmeal fed trout. Highest (P < 0.05) hepatic Cu concentrations were also observed in trout fed plant-based diets. No differences (P >0.05) were observed in growth or hepatic concentrations due to Cu source. From experiment two, no antagonistic interactions were observed between increasing levels of dietary Zn and Cu. Trout fed the two highest levels of dietary Zn (300 and 1500 ppm) had the greatest (P < 0.05) weight gains. Dietary Zn supplementation increased (P < 0.05) whole body Cu at 12 wks. With increasing dietary Zn supplementation, resulted in increased (P < 0.05) whole body Zn. Cataracts and tail rot were observed at 12 wks in trout fed the Cu and Zn deficient diet. In conclusion, plant-based diets enhanced Cu bioavailability indicated by higher weight gains and hepatic Cu concentrations in experiment one, compared to trout fed fishmeal-based diets. Cu supplementation is required in a plant-based in order to achieve optimal growth in trout. Results of the second study indicate rainbow trout fed plant-based diets require Zn supplementation to obtain sufficient growth. The highest levels of Zn supplementation did not impair Cu uptake in rainbow trout.Item Evaluation of the nutritional value of ethanol yeast in practical-type diets as an alternative protein source for rainbow trout Oncorhynchus mykiss(Montana State University - Bozeman, College of Agriculture, 2012) Hauptman, Blake Stewart; Chairperson, Graduate Committee: John Paterson.Ethanol yeast (EY) is a single-cell protein obtained as a co-product during the production of fuel ethanol and may have potential as an alternative protein source for rainbow trout. The objective of the current study was to determine if EY could replace fish meal (FM) without negatively impacting growth performance of juvenile rainbow trout. Three experiments were conducted to evaluate the use of EY. In Exp. 1 a digestibility trial was done to determine EY apparent digestibility coefficients (ADCs) for protein, lipid, energy, DM, and apparent availability coefficients (AACs) for amino acids. In Exp. 2 a feeding trial was conducted where a control diet (42% digestible protein and 20% crude lipid) was compared to diets where FM digestible protein was replaced by EY at varying levels (25, 37.5, 50, 62.5, 75, 87.5, and 100%). Diets were fed twice daily to rainbow trout to apparent satiation in a 15°C recirculating system. There were 4 replicate tanks per diet (30 fish/tank). Experiment 3 was conducted to determine if a mycotoxin inhibitor (Biofix Plus) could improve performance of rainbow trout when fed higher levels of EY. The experiment was a 2x3 factorial where FM was replaced with EY (0, 50 and 100%) with or without Biofix Plus. There were three replicate tanks per diet (15 fish/tank). Results from Exp. 1 showed that Ethanol yeast ADCs for protein, DM, lipid, energy and AAC for and sum of amino acids were quantified at 98, 65, 100, 70, 81 and 81%, respectively. Results from Exp. 2 showed that fish growth was not different from the control diet at the 25% and 37.5% replacement levels. However, reduced growth (P < 0.001) and poorer feed conversion (P < 0.001) were measured when EY replaced more than 37.5% of dietary FM (11.2% EY inclusion). Results from Exp. 3 found no effect of Biofix Plus on performance of rainbow trout. There was reduced growth (P=0.001) in the 50 and 100% replacement diets. Apparent digestibility coefficients suggested that EY nutrients were highly digestible. However, growth was reduced at EY inclusion levels that were greater than 11.2%.