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

养殖鱼在每个生长季节的健康取决于包括当地环境条件在内的一系列因素，其中许多因素与水温和水质有关。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，所有这些对鱼类健康都至关重要。除了水温外，最佳的饲喂对确保良好的生长速度、健康的免疫系统、食品的整体质量及其市场适宜性至关重要。随着海水温度变暖，水产养殖业面临着三文鱼夏季肠道综合症(SGS)的增加，这种情况导致饲料同化不良，降低了生长效率。Cermaq Canada是三文鱼水产养殖业的世界领先者，该公司正在考虑改用高温(HT)鱼饲料，以减少当地温哥华岛三文鱼养殖场的SGS，这种饲料在高水温下可能表现得更好。鉴于这种新饲料的财务成本增加，该公司急于验证他们特定的养殖地点，对鱼类生长和一般健康的好处超过了HT饲料增加的成本。在他们的验证中，该公司要求我的实验室的专业知识来评估与传统和新型高温饲料相关的鲑鱼肠道微生物群的差异。我的实验室将通过对这两种饲料的16SrRNA基因V4-V5可变区扩增片段进行Illumina标签测序，提供鱼肠道微生物群的详细特征。提交给该公司的书面报告将包括通过QIIME管道进行的数据分析，然后对结果进行统计分析。此外，我们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在每个被分析的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.