Multi-method investigation and characterization of the ocular microbiome

眼部微生物组的多方法研究和表征

• 批准号: 10660691
• 负责人: ROBERT A BRITTON
• 金额: $ 66.33万
• 依托单位: BAYLOR COLLEGE OF MEDICINE
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-07-01 至 2026-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10660691
• 关键词: Archaea; Automobile Driving; Bacteria; Biological Assay; Biology; Biomass; Carbon; Cell Culture Techniques; Cell physiology; Cells; Communities; Coupled; Development; Diet; Ecology; Environment; Eye; Fractionation; Genes; Genome; Goals; Growth; Health; Human; Human Microbiome; Human body; Immune response; Immune system; Immunology; Individual; Inflammation; Intestines; Investigation; Large Intestine; Length; Metagenomics; Methods; Microbe; Monitor; Oral cavity; Peripheral Blood Mononuclear Cell; Persons; Physiology; Pilot Projects; Resources; Ribosomal DNA; Sampling; Shapes; Shotguns; Site; Skin; Source; Sterility; Structure; Techniques; United States National Institutes of Health; Whole-Genome Shotgun Sequencing; Work; antimicrobial; commensal bacteria; conjunctiva; corneal epithelium; fungus; immune function; metabolomics; metagenome; metagenomic sequencing; microbial; microbial community; microbial products; microbiome; microbiome composition; microbiome research; multidisciplinary; multiple omics; novel; ocular microbiome; ocular surface; response; tool; whole genome

The human body is host to trillions of commensal bacteria, archaea, and fungi whose total gene content is estimated to be over 2000 times more than that of their human hosts, most of which reside in the intestinal tract and colonize many other body sites, notably skin and mouth. The Human Microbiome Project, launched in 2007 by the NIH, has been instrumental in driving the development of multi-omic tools to characterize microbiomes, however the vast majority of studies have focused on studying the microbiome of the large intestine. Moreover, these studies have served to simply sequence these communities, with little effort put forth to cultivate and functionally characterize them or their individual bacterial strains. Therefore, cultivation and characterization of microbial communities at sites less well studied than the gut is a key, unmet need in the field of microbiome research. The ocular surface was initially thought to be sterile due to difficulty in obtaining viable microbes using traditional culture-based techniques, not to mention the potent anti-microbial defenses present in tears. Recent work has indicated the ocular surface is not sterile but contains a low biomass microbial community, which suggests these microbes may play a role in ocular health. However, because most studies characterizing the eye microbiome have focused solely on 16S rDNA and metagenomic sequencing to date, the presence of a bona fide ocular microbiome is still poorly understood. In response to this U24 RFA, we propose to better define the breadth of microbes and microbial communities that populate the ocular surface through a combination of targeted cultivation and metagenomic sequencing approaches. Once individual microbes and communities have been cultivated and cataloged, we will functionally assess the impact of these microbes on various aspects of human eye biology. We have assembled a multidisciplinary team with complementary expertise in ocular biology, immunology, microbial ecology and physiology, metagenomics and microbial cultivation to generate robust resources of microbial strains, genomes, metagenomes, and functional repertoire for the eye and microbiome communities. The following goals to be pursued in generating these resources are: Goal 1: Cultivation and characterization of the ocular surface microbiome. We will use a combination of targeted cultivation, full length (FL) 16S rDNA sequencing, and whole genome shotgun (WGS) metagenomics to characterize the microbiomes associated with the ocular surface including the conjunctiva, tears, and periocular skin. Goal 2: Functional characterization of microbes and microbial community interactions with the eye. To understand how eye associated microbes can impact eye health and physiology, we will combine cultivation of individual microbes from the ocular surface with primary human cell culture assays to monitor the functional impact of microbes on the eye. Our ultimate goal by the end of this proposal period is to have a robust set of well-characterized ocular surface microbes with which the scientific community can now begin functional characterization of eye/microbiome interactions.

人体是数万亿共生细菌、古细菌和真菌的宿主，其总基因含量为 据估计比人类宿主多2000多倍，其中大部分存在于肠道中 并定植于许多其他身体部位，尤其是皮肤和口腔。人类微生物组计划，2007 年启动 由美国国立卫生研究院 (NIH) 开发，在推动多组学工具的开发来表征微生物组方面发挥了重要作用， 然而，绝大多数研究都集中在研究大肠的微生物组。而且， 这些研究只是对这些群落进行了简单的排序，几乎没有付出什么努力来培养和 对它们或它们各自的细菌菌株进行功能表征。因此，培养和表征 与肠道相比研究较少的部位的微生物群落是微生物组领域一个关键的、未满足的需求 研究。眼表最初被认为是无菌的，因为很难使用微生物获得活微生物。 基于传统文化的技术，更不用说眼泪中存在的强大的抗菌防御能力。最近的 研究表明，眼表面并非无菌，而是含有低生物量的微生物群落， 表明这些微生物可能在眼部健康中发挥作用。然而，由于大多数研究都描述了 迄今为止，眼部微生物组仅关注 16S rDNA 和宏基因组测序， 真正的眼部微生物组仍然知之甚少。为了回应 U24 RFA，我们建议更好地定义 微生物和微生物群落的广度通过以下方式的组合而填充在眼表面 靶向培养和宏基因组测序方法。一旦单个微生物和群落形成 经过培养和编目后，我们将从功能上评估这些微生物对各个方面的影响 人眼生物学。我们组建了一支多学科团队，在眼科领域具有互补的专业知识 生物学、免疫学、微生物生态学和生理学、宏基因组学和微生物培养 丰富的微生物菌株、基因组、宏基因组和眼睛和功能库的资源 微生物群落。生成这些资源要实现的目标如下： 目标 1： 眼表微生物组的培养和表征。我们将使用有针对性的组合 培养、全长 (FL) 16S rDNA 测序和全基因组鸟枪法 (WGS) 宏基因组学 描述与眼表相关的微生物组，包括结膜、泪液和眼周 皮肤。目标 2：微生物的功能表征以及微生物群落与眼睛的相互作用。 为了了解与眼睛相关的微生物如何影响眼睛健康和生理机能，我们将结合培养 通过原代人类细胞培养测定对来自眼表面的单个微生物进行监测，以监测其功能 微生物对眼睛的影响。我们的最终目标是在本提案期结束时拥有一套强大的 科学界现在可以开始对眼表微生物进行功能性表征 眼睛/微生物组相互作用的表征。