The influences of diet and water systems on rainbow trout gut microbiome in relation to nutrient utilization

Abstract

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.