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.

人体占据了数万亿个共生细菌，古细菌和真菌，其总基因含量为 估计比其人类宿主高2000倍，其中大多数位于肠道中 并殖民许多其他身体部位，尤其是皮肤和口腔。人类微生物组项目，于2007年启动 由NIH撰写，有助于推动多摩变工具的开发来表征微生物， 但是，绝大多数研究都集中在研究大肠的微生物组。而且， 这些研究简单地简单地对这些社区进行了排序，几乎没有努力培养和 在功能上表征它们或它们的单个细菌菌株。因此，培养和表征 在微生物组领域，与肠道相比，所研究的地点的微生物群落不足是未满足的关键需求 研究。最初认为眼表面是无菌的，因为难以获得可行的微生物 传统的基于文化的技术，更不用说泪流满面的有力的反微生物防御。最近的 工作表明，眼表面不是无菌的，但含有低生物质微生物群落， 建议这些微生物可能在眼部健康中发挥作用。但是，因为大多数表征的研究 眼睛微生物组仅集中在16S rDNA和元基因组测序上，迄今为止的存在 善意的眼微生物组仍然很少了解。为了响应此U24 RFA，我们建议更好地定义 通过组合的微生物和微生物群落的广度 靶向培养和宏基因组测序方法。一旦个人微生物和社区拥有 已被培养和分类，我们将在功能上评估这些微生物对 人眼生物学。我们已经组建了一个具有互补专业知识的多学科团队 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以产生 微生物菌株，基因组，宏基因组和功能库的强大资源 微生物组社区。生成这些资源时要追求的以下目标是：目标1： 眼表微生物组的培养和表征。我们将使用目标的组合 培养，全长（FL）16S rDNA测序以及整个基因组shot枪（WGS）宏基因组学 表征与眼表相关的微生物组，包括结膜，眼泪和眼周 皮肤。目标2：微生物和微生物群落与眼睛的相互作用的功能表征。 为了了解眼睛相关的微生物如何影响眼睛的健康和生理，我们将结合种植 来自眼表面的单个微生物，具有原代人类细胞培养分析，以监测功能 微生物对眼睛的影响。在这个提案期结束时，我们的最终目标是拥有一组健壮的 特征良好的眼表微生物现在可以开始使用该微生物 眼/微生物组相互作用的表征。