The role of the gut microbiome on the health and nutrition of salmonid fishes

加拿大各地有成千上万的孵化场，它们将鱼类储存在河流和湖泊中，用于保护、钓鱼和农业目的。然而，在过去的40年里，成功放养率一直很低，需要新的策略来改善放养到野外和网笼养殖场的鲑鱼的生长、健康和生存。抗生素的使用继续受到限制，尽管孵化场仍然依赖抗生素来治疗疾病和避免死亡事件。因此，需要提高抗病能力和放养成功率的替代战略，在不使用抗生素的情况下保护未来的野生种群和食用鱼生产。肠道微生物群被认为是一种代谢“器官”，它将膳食纤维发酵成短链脂肪酸和代谢物，为宿主提供能量，与免疫系统相互作用，并刺激肠道发育。最近，我的研究是第一个绘制鲑鱼类鱼类肠道微生物群的研究之一，如虹鳟鱼和大西洋鲑鱼，使用下一代16S rDNA测序。我的研究发现了饮食、氧气和温度对鱼类肠道微生物组成的显著影响，但缺乏对其对生长性能、健康和生存的后续影响的研究。我研究的短期目标是结合前沿的体内和体外技术来评估肠道微生物组营养物质对鱼类的贡献以及饮食、生命阶段和遗传家族的影响。长期目标是开发益生菌和饲料配方，增强鱼类的肠道微生物群和免疫反应，以改善野生和养殖鱼类的健康和放养成功。为了实现这些目标，我的研究计划的目标是：1)通过对20+ 16S rDNA数据集的荟萃分析，对影响鲑科鱼类肠道微生物组的环境/宿主因素的重要性进行排序；2)通过体外模型，量化野生和养殖鱼类肠道微生物中脂肪酸、维生素、氨基酸和其他代谢物的产量；3)通过体内生长试验，确定饲粮中添加益生菌对养殖鱼类生长性能和饲料利用率的影响；喂食抗生素和/或益生菌后体内细菌攻击的免疫和微生物组反应，以及5)不同遗传家族和生命阶段的宿主效应与野生鱼类肠道微生物和表型性状的相关性。这项研究基于一种新颖而全面的策略，该策略将结合先进的营养、微生物学和基因组学技术，以更好地了解肠道微生物组的潜在机制。该计划将直接惠及众多终端用户，如渔业、养鱼场和政府机构，以及依赖鱼类作为重要营养来源和文化认同的公众和土著社区。

Thousands of hatcheries are relied upon across Canada to stock fish into in rivers and lakes for conservation, sport fishing and farming purposes. However, successful stocking rates during the past 40 years have been low and new strategies are needed to improve growth, health and survival of salmonid fishes released into the wild and net-pen farms. Antibiotic use continues to be restricted, although they are still relied upon in hatcheries to treat disease and avoid mortality events. Therefore, alternative strategies that improve disease resistance and stocking success are require to protect future wild stocks and food fish production without using antibiotics. The gut microbiome is considered to be a metabolic "organ" that ferments dietary fibres into short-chain fatty acids and metabolites that contribute energy to the host, interact with the immune system and stimulate gut development. Recently, my research was one of the first to map the gut microbiome of salmonid fishes, such as rainbow trout and Atlantic salmon, using next-generation sequencing of 16S rDNA. My research has found significant impacts of diet, oxygen and temperature on the composition of gut microbes in fish, although research is lacking on their subsequent effects on growth performance, health and survival. The short-term goal of my research is to use a combination of cutting-edge in vivo and in vitro techniques to assess the contribution of nutrients from the gut microbiome to fish and influences from diet, life-stage and genetic family. The long-term goal is to develop probiotic and feed formulations that enhance the gut microbiome and immune response of fish to improve health and stocking success of both wild and farmed fish. To address these goals, the objectives of my research program are to: 1) rank the significance of environmental/host factors that impact the gut microbiome of salmonid fishes through meta-analysis of 20+ 16S rDNA datasets, 2) quantify the production of fatty acids, vitamins, amino acids and other metabolites from gut microbes from wild and farmed fish using an in vitro model, 3) determine dietary effects of feeding probiotics on the growth performance and feed utilization of farmed fish through an in vivo growth trial, 4) assess the gut physiology, immune and microbiome responses after feeding antibiotics and/or probiotics followed by an in vivo bacterial challenge, and 5) correlate host effects of different genetic families and life-stages with gut microbes and phenomic traits of wild fish. This research is based on a novel and comprehensive strategy that will combine advanced nutritional, microbiological and genomics techniques to better understand underlying mechanisms of the gut microbiome. This program will directly benefit numerous end-users, such as fisheries, fish farms and government agencies, as well as the general public and Indigenous communities that rely on fish for a vital source of nutrients and cultural identity.