Characterizing the modification of the gut microbiome of farmed salmon as a function of feeding regimes designed to reduce summer gut syndrome in British Columbia salmon farms

养殖鱼类在每个生长季节的健康状况取决于一系列因素，包括当地的环境条件，其中许多与水温和水质有关。水温对溶解氧、浮游植物水华和微生物生物量等其他重要条件有很大影响，这些条件对鱼类健康至关重要。除了水温，最佳的喂养是至关重要的，以确保良好的生长速度，健康的免疫系统，以及食品的整体质量和市场需求。随着海水温度的升高，水产养殖业面临着鲑鱼夏季肠道综合征（SGS）的增加，这种情况导致饲料吸收不良，生长效率降低。Cermaq Canada是鲑鱼水产养殖的世界领先者，正在考虑改用高温（HT）鱼饲料，以减少其当地温哥华岛鲑鱼养殖场的SGS，这种饲料在高水温下可能表现更好。考虑到这种新饲料增加的财务成本，该公司渴望验证其特定的养殖地点，对鱼类生长和一般健康的好处超过HT饲料增加的成本。在验证过程中，该公司要求我的实验室提供专业知识，以评估与传统和新型HT饲料相关的鲑鱼肠道微生物组的差异。我的实验室将通过Illumina标签测序两种类型饲料的16 SrRNA基因V4-V5可变区扩增子来提供鱼肠道微生物组的详细表征。向公司提交的书面报告将包括通过QIIME管道进行的数据分析，以及对结果的统计分析。此外，我们还将为该公司提供一个可搜索的序列类型数据库（操作分类单位或OTU）及其相关的主OTU表，其中包含这些OTU在分析的每个鱼肠道样本中的相对丰度数据。

The health of farmed fish in each growing season depends on a suite of factors including local environmentalconditions, many of which are correlated with water temperature and quality. Water temperature has a stronginfluence on other important conditions such as dissolved oxygen, phytoplankton bloom and microbialbiomass, all vitally important for fish health. Aside from water temperature, optimal feeding is critical ininsuring good growth rate, a healthy immune system, and the overall quality of the food product and its marketdesirability. With warming seawater temperature, the aquaculture industry faces an increase in summer gutsyndrome (SGS) in salmon, a condition that leads to poor assimilation of the feed, and reduced growthefficiency. Cermaq Canada, a world leader in salmon aquaculture, is engaged in reducing SGS in their localVancouver Island salmon farms by considering a switch to a high temperature (HT) fish feed that may performbetter in high water temperatures. Given the increased financial costs of this new feed, the company is eager tovalidate for their specific farming location, that benefits to fish growth and general health outweigh the increasecost of the HT feed. In their validation, the company has requested the expertise of my laboratory to assess thedifferences in the salmon gut microbiome associated with the conventional and novel HT feed. My laboratorywill provide a detailed characterization of the the fish gut microbiome by Illumina Tag-sequencing of the 16SrRNA gene V4-V5 variable region amplicons for both types of feed. A written report to the company willinclude the data analysis through the QIIME pipeline, followed by a statistical analysis of the results. Inaddition, we will provide the company with a searchable database of the sequence types (operational taxonomicunits or OTUs) and its associated Master OTU table containing the relative abundance data of these OTUs ineach fish gut sample analysed.