Metabolic Syntrophy Between Human Gut Bacteria and Archaea

摘要 这项拟议研究的目标是确定微生物合成的分子代谢信号 人类肠道，长期目标是开发一种预测模型，将宿主饮食与健康的肠道微生物区系联系起来 恢复力。具体地说，在项目负责人的实验室进行的研究旨在识别和表征 人类共生菌类杆菌代谢产物和基因的生理功能 在一部小说中，细菌(B.theta)和产甲烷的史密甲烷短杆菌(M.smithii) 共培养体系。B.theta和M.smithii是人类肠道中的优势细菌和古细菌， 它们的代谢是相互依赖的；已知两者都与肠道上皮细胞有关。 类杆菌和/或甲烷短杆菌种群的扰动与肥胖、厌食症、 肠易激疾病、克罗恩病、结直肠癌和憩室病。出于这些原因，该项目 Leader假设两种生物之间的代谢合成对健康的肠道功能和 饮食或病原体挑战会扰乱联会，导致消化障碍和传染病。三 提出了使用一种新的共培养系统来检验这一假说的具体目标。在具体目标1中， 项目负责人将优化B.theta/M.smithii共培养系统。具体地说，她将使用厌氧 用微生物学技术确定细菌合养连续共培养的营养需求 在人体肠道中遇到的条件下，恒化和测试营养增强。她还将使用 光学和共聚焦荧光显微镜研究空间组织(浮游或与之相关的 两种生物的聚集体)共培养。在具体目标2中，项目负责人将创建一个完整的 基于代谢组和转录组数据的共培养合并体代谢模型。具体来说，她将 使用下一代测序技术(RNAseq)识别由两者上调的基因转录本 在共养共培养中提高代谢系统模型的准确性。系统型号将 通过全球和靶向代谢组学数据进行验证。精细化的系统模型，集成转录 和代谢组学数据集，将被用于预测病原体挑战如何影响合并症 B.theta/M.smithii代谢。最后，在具体目标3中，项目负责人将测试共同文化的弹性，以 病原体挑战赛。她将测量在共培养过程中发生的代谢和转录变化。 系统受到小鼠肠道病原体肠道出血性罗氏柠檬酸杆菌的攻击。这些 将通过实验进一步提炼和测试针对特定目标生成的系统模型2。 这项研究的创新成果将证明B.theta和M.smithiii在共培养中 通过小分子代谢物的双向交换进行交流。添加一种病原体是 预计会扰乱这一通讯系统。这项工作意义重大，因为它将证明 对人类健康和疾病有贡献的常见肠道微生物之间的融合。

ABSTRACT The goal of the proposed research is to identify molecular metabolic signals of microbial syntrophy in the human gut, with the long-term goal of developing a predictive model relating host diet to healthy gut microbiota resiliency. Specifically, the research in the project leader's laboratory aims to identify and characterize the physiological function of metabolites and genes produced by human symbiotes Bacteroides thetaiotaomicron (B. theta), a bacterium, and Methanobrevibacter smithii (M. smithii), a methane-producing archaeon, in a novel co-culture system. B. theta and M. smithii are the dominant bacterium and archaeon in the human gut, respectively; their metabolisms are interdependent; and both are known to associate with gut epithelia. Perturbation of Bacteroides and/or Methanobrevibacter populations is associated with obesity, anorexia, irritable bowel disease, Crohn's disease, colorectal cancer, and diverticulosis. For these reasons, the project leader hypothesizes that metabolic syntrophy between both organisms is essential for healthy gut function and diet or pathogen challenge disrupts syntrophy, leading to digestive disorders and infectious disease. Three specific aims are proposed to test this hypothesis using a novel co-culture system. In Specific Aim 1, the project leader will optimize a B. theta/M. smithii co-culture system. Specifically, she will use anaerobic microbiology techniques to define the nutritional requirements of a syntrophic continuous co-culture in a chemostat and test nutritional enhancements under conditions encountered in the human gut. She will also use optical and confocal fluorescence microscopy to study the spatial organization (planktonic or associated in aggregates) of both organisms in co-culture. In Specific Aim 2, the project leader will create an integrated metabolic model of co-culture syntrophy based on metabolomic and transcriptomic data. Specifically, she will use next-generation sequencing technology (RNAseq) to identify gene transcripts upregulated by both organisms in syntrophic co-culture to improve accuracy of the metabolic system models. The system model will be validated with global and targeted metabolomics data. The refined system model, integrating transcriptomic and metabolomics datasets, will be used to predict how pathogen challenge affects syntrophic B.theta/M.smithii metabolism. Finally, in Specific Aim 3, the project leader will test co-culture resiliency to pathogen challenge. She will measure the metabolic and transcriptional changes that occur in the co-culture system when challenged by the mouse gut pathogen enterohemorrhagic Citrobacter rodentium. These experiments will be used to further refine and test the system model generated in Specific Aim 2. The innovative outcome of this research will be the demonstration that B. theta and M. smithiii in co-culture communicate through the two-way exchange of small molecule metabolites. Addition of a pathogen is expected to disrupt this communication system. This work is highly significant in that it will demonstrate syntrophy between common gut microbes that contribute to human health and disease.