Multi-omics characterization of HIV-associated changes in the gut microbiome and host mucosal immunity

项目摘要 人类肠道中有着极其多样的肠道微生物群落，它们与人类的微生物共同进化， 帮助人体发挥重要的代谢和免疫功能。微生物组的变化对 糖尿病、肥胖、免疫缺陷和炎症性肠病（IBD）等多种疾病状态仅 现在被认出来了。人类免疫缺陷病毒（HIV）感染对肠道有深远的影响， 感染的标志是肠道相关的CD 4 + T细胞的快速消耗， 淋巴组织（GALT）和肠上皮屏障功能受损。尽管如此，我们的理解 HIV感染时肠道菌群的变化以及这些变化对宿主的潜在影响 免疫力和艾滋病毒疾病进展仍然不完全，特别是在撒哈拉以南非洲的人口中， 那里的艾滋病负担最重。我们之前发表的工作是为数不多的研究艾滋病毒的研究之一- 撒哈拉以南非洲地区肠道微生物组的相关变化。已发表的HIV研究的局限性- 肠道微生物组的相关改变包括1）使用16 S rRNA基因测序来鉴定细菌 分类群丰富，但未能解决菌株水平的差异，2）缺乏深层功能表征 3）仅在发达地区对艾滋病毒感染人群进行表征，4）缺乏 与机械实验的结合。我们的建议通过以下方式解决了该领域的局限性：1）使用 全面的培养组学、宏基因组学、元转录组学和代谢组学方法， 在菌株水平上表征肠道微生物组，2）评估其功能，3）整合美国 人群沿着来自撒哈拉以南非洲的受试者，那里的HIV负担最大，并且已知 基线肠道微生物群与生活在发达地区的人有很大不同，4）整合这些微生物群， 使用体外和离体模型进行机理研究分析。总的来说，独特的，好的- 使用结合了联合收割机计算和免疫学的尖端检测方法分析特征化的人类样本， 这种方法是高度创新的，将寻求识别影响艾滋病毒的细菌菌株、基因和分子 在美国和撒哈拉以南非洲的疾病。这项工作还将导致产生一个多'omic 一个数据库，将作为该领域的资源，包括社区对数据和细菌菌株的访问 从本项目分析的样品中分离。

PROJECT SUMMARY The human gut harbors an enormously diverse community of commensal microbes that has co-evolved with humans to assist in critical host metabolic and immune functions. The impact of changes in the microbiome on disease states as diverse as diabetes, obesity, immunodeficiency, and inflammatory bowel disease (IBD) is only now being recognized. Human immunodeficiency virus (HIV) infection has profound effects on the intestinal mucosal environment with a hallmark of infection being a rapid depletion of CD4+ T cells within gut associated lymphoid tissue (GALT) and impairment of intestinal epithelial barrier function. Despite this, our understanding of intestinal microbiota changes occurring with HIV infection and the potential effects of these changes on host immunity and HIV disease progression remains incomplete, particularly in populations in sub-Saharan Africa, where HIV disease burden is greatest. Our prior published work is one of only a few studies to examine HIV- associated changes in the gut microbiome in sub-Saharan Africa. Limitations of published studies of HIV- associated alterations in the gut microbiome include 1) the use of 16S rRNA gene sequencing to identify bacterial taxa abundances but failure to resolve differences at the strain level, 2) lack of deep functional characterization of bacterial communities, 3) characterization of HIV-infected populations in developed regions only, and 4) lack of integration with mechanistic experiments. Our proposal addresses the limitations in the field by 1) using comprehensive culturomic, metagenomic, metatranscriptomics, and metabolomic approaches to fully characterize the gut microbiome at the strain level, 2) assessing its function, 3) integrating studies of a U.S. population along with subjects from sub-Saharan Africa, where HIV burden is greatest and where it is known that baseline gut microbiota differ significantly from those living in developed regions and 4) integrating these analyses with mechanistic studies using in vitro and ex vivo models. Overall, the combination of unique, well- characterized human samples analyzed with cutting-edge assays that combine computational and immunologic approaches is highly innovative and will seek to identify bacterial strains, genes, and molecules that impact HIV disease in the U.S. and sub-Saharan Africa. This work will additionally lead to the generation of a multi-‘omic database that will serve as a resource for the field, including community access to data and bacterial strains isolated from samples analyzed in this project.