EAGER: Initial characterization of the elasmobranch microbiome and potential roles in host physiology

EAGER：软骨鱼类微生物组的初步表征及其在宿主生理学中的潜在作用

• 批准号: 1419206
• 负责人: Darrell Grimes
• 金额: $ 28.99万
• 依托单位: University of Southern Mississippi
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-05-15 至 2017-04-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1419206&HistoricalAwards=false
• 关键词: EAGER; Initial; characterization; elasmobranch; microbiome

Beneficial relationships between vertebrates and bacteria have been the subject of intense study, and it is now well established that bacterial communities (microbiomes) of the skin, mouth and digestive system play critical roles in host metabolism and overall health. However, in perhaps the most unique and yet understudied vertebrate-bacteria relationship, evidence suggests that bacteria reside within the blood and organs of healthy sharks, skates and stingrays (elasmobranch fishes). To our knowledge the widespread presence of bacteria within the tissues and organs of a healthy vertebrate is unprecedented, and therefore characterizing the elasmobranch microbiome will provide valuable insight into the evolution of vertebrate immunity and microbial symbioses. This project will provide multidisciplinary graduate student training in elasmobranch biology, bioinformatics and cutting-edge molecular techniques at both the University of Southern Mississippi and the J. Craig Venter Institute.While previous studies were limited to the identification of bacterial species that could be cultured, this project will use 16S rRNA gene sequencing to identify bacteria present in the blood, kidney and liver of two common species of elasmobranch, the Atlantic stingray and the Atlantic sharpnose shark. The investigators will also validate for the first time the existence and specific locations of these bacteria within tissues using molecular methods as well as transmission electron microscopy. The amplified 16S rRNA genes will allow rRNA gene library construction and bridge amplification. Sequencing will be completed using the MiSEQ platform by Illumina. Analysis and estimation of phylogenetic diversity of 16S rDNA sequence data will be accomplished with clustered high quality trimmed sequences. It is expected that results will verify the presence, location and identity of bacteria within elasmobranch tissues, establishing a new and paradigm-shifting model for the study of vertebrate-bacteria relationships including host metabolism, self-recognition, and immune system function.

脊椎动物和细菌之间的有益关系一直是深入研究的主题，现在已经确定皮肤，口腔和消化系统的细菌群落（微生物组）在宿主代谢和整体健康中起着关键作用。然而，在也许是最独特的，但研究不足的脊椎动物-细菌的关系，有证据表明，细菌存在于健康的鲨鱼，冰鞋和黄貂鱼（板鳃类鱼类）的血液和器官。据我们所知，细菌在健康脊椎动物的组织和器官内的广泛存在是前所未有的，因此表征板鳃类微生物组将为脊椎动物免疫和微生物共生的进化提供有价值的见解。该项目将在南密西西比大学和J.克雷格文特尔研究所为研究生提供多学科的板鳃类生物学、生物信息学和尖端分子技术培训。虽然以前的研究仅限于鉴定可培养的细菌种类，但该项目将使用16 S rRNA基因测序来鉴定血液中存在的细菌，两种常见的板鳃类动物大西洋黄貂鱼和大西洋尖鼻鲨的肾脏和肝脏。研究人员还将首次使用分子方法和透射电子显微镜验证这些细菌在组织中的存在和具体位置。扩增的16 S rRNA基因将允许rRNA基因文库构建和桥式扩增。测序将使用Illumina的MiSEQ平台完成。16 S rDNA序列数据的系统发育多样性分析和估计将通过聚类的高质量修剪序列来完成。预计结果将验证板鳃类组织内细菌的存在，位置和身份，建立一个新的和范式转移的脊椎动物-细菌关系，包括宿主代谢，自我识别和免疫系统功能的研究模型。