Metaproteomics to investigate intestinal microbiota-host and -diet interactions

项目摘要/摘要 在凯鹏华盈的实验室里，我们研究了微生物共生体和宿主的新陈代谢、生理和相互作用。 相关的微生物区系。为此，我们结合了多种独立于栽培的方法，例如 元基因组学、代谢组学、元蛋白质组学和单细胞成像--以培养为基础的方法 包括外源基因表达、生化检测等体外检测。我们的研究 专注于高分辨率质谱学驱动的代谢蛋白质组学的发展 寄主相关微生物区系中蛋白质的大规模鉴定和定量。 在接下来的五年里，我计划继续使用这些方法来研究肠道微生物区系反应 与外部底物(日粮)和宿主衍生底物(宿主化合物)的相互作用及其机制 觅食)。我假设不同的饮食蛋白质来源和宿主衍生的化合物会有很大的 对微生物区系的不同影响，因此在研究饮食的相互联系时需要考虑， 微生物区系，和宿主健康。我建议使用元蛋白质组学，辅之以元基因组学和 代谢组学，以(1)确定和量化微生物组成员使用和转化的底物 以及(2)确定这些底物如何影响群落组成以及与其他底物的功能相互作用 微生物区系成员和宿主。这项研究将提供对功能的迫切需要的洞察 通过优化和部署新的方法来影响肠道微生物区系消耗的底物 寄主、饮食和肠道微生物蛋白质的可重复性、大规模表征。 我的长期目标是开发元蛋白质组学方法，使我们能够定量地和可重复性地 确定微生物群落的功能相互作用，并定义微生物群落之间的关键相互作用 微生物区系和饮食蛋白质将为治疗干预措施的发展提供信息。这些 方法也将是研究与人类微生物群有关的任何疾病的强大工具 在不同的身体部位和微生物群落上，人类在他们的环境中与之相互作用 可能会影响健康。

Project Summary/Abstract In the Kleiner laboratory we study metabolism, physiology and interactions in microbial symbioses and host- associated microbiota. For this we combine a diversity of cultivation independent approaches – such as metagenomics, metabolomics, metaproteomics and single cell imaging – with cultivation-based approaches including heterologous gene expression, biochemical assays and other in vitro measurements. Our research has a strong focus on the development of high-resolution mass spectrometry driven metaproteomics for the large-scale identification and quantification of proteins in host-associated microbiota. During the next five years, I plan to continue using these approaches to study intestinal microbiota responses to, and mechanisms of interaction with, external substrates (diet) and host-derived substrates (host compound foraging). I hypothesize that different dietary protein sources and host-derived compounds will have vastly different impacts on the microbiota and thus need to be considered when studying the interconnection of diet, the microbiota, and host health. I propose to use metaproteomics, complemented with metagenomics and metabolomics, to (1) identify and quantify the substrates that are used and converted by microbiota members and (2) determine how these substrates impact community composition and functional interactions with other microbiota members and the host. This research will provide urgently needed insight into the functional impacts of substrates consumed by gut microbiota by optimizing and deploying novel approaches for the reproducible, large-scale characterization of host, diet and microbial proteins in the intestinal tract. My long-term goals are to develop metaproteomic approaches that allow us to quantitatively and reproducibly determine functional interactions in microbial communities, and to define critical interactions between the microbiota and dietary proteins that will inform the development of therapeutic interventions. These approaches will also be powerful tools for studying any disease associated with the human microbiome in and on different body sites and microbial communities that humans interact with in their environment and that potentially impact health.