Integrating time, function, phylogenetics and genome dynamics to redefine microbial diversity

整合时间、功能、系统发育学和基因组动力学，重新定义微生物多样性

• 批准号: RGPIN-2017-05141
• 负责人: Beiko, Robert
• 金额: $ 2.91万
• 依托单位: Dalhousie University
• 依托单位国家: 加拿大
• 项目类别: Discovery Grants Program - Individual
• 财政年份: 2020
• 资助国家: 加拿大
• 起止时间: 2020-01-01 至 2021-12-31
• 项目状态: 已结题
• 来源: https://www.nserc-crsng.gc.ca/ase-oro/Details-Detailles_eng.asp?id=710708
• 关键词: Integrating; time; function; phylogenetics; genome

Thanks to advances in DNA sequencing technology and bioinformatics, we know more about microorganisms and microbial communities than ever before. Work in the last thirty years has revealed a stunning diversity of microbes in every habitat on Earth, and researchers are now trying to connect this diversity to ecosystem function in settings as varied as wastewater reactors and the human gut. Understanding the microbes in a given habitat (the microbiome) opens up new applications including mitigation of human disease and remediation of contaminated sites. Although this “microbial revolution” has great promise, researchers struggle to understand the microbiome in depth. The remarkable diversity of microbial species, which can exceed 1,000 in a single environmental sample, is a significant barrier to understanding the ecology of a system. Many habitats also contain millions of distinct microbial genes, a number that dwarfs the 20,000-25,000 genes in the human genome. However, the most critical limiting factor is that we don't know what patterns to look for when we examine microbial communities. Methods that presuppose natural groupings such as species inevitably miss important patterns in the data, and we need to expand our microbiomics toolbox with new representations of microbial diversity. My research program is concerned with diversity and evolution of the microbiome. This proposal encompasses two complementary projects that will advance our ability to deconstruct and describe microbial communities. First, we will develop new ecological models that treat individual genes as species, and represent an organism as an entire ecosystem in which these genes interact. This “gene ecology” model will allow us to map traditional concepts such as diversity, dispersal, and competition into the study of microbial genomes. Second, we will develop new definitions of biodiversity units that are based on covariance through time, co-occurrence in multiple habitats, similar functions and ecological roles, as well as traditional taxonomic similarity. These new definitions will produce a prohibitively large number of candidate units, and we will develop new approaches to identify and interpret the candidates that are most relevant to a particular ecological question. Microbial gene ecology will provide a better understanding of the complex interactions between gene products in the microbiome, and an expanded set of candidate units will help us better evaluate changes in microbial community composition. Taken together, these techniques will tell us which members of a microbial community are playing which roles, how different members of the community are interacting with one another, and how communities are likely to respond to changes in their environment. This understanding will be essential as we try to develop microbial solutions to a host of problems in human health and the environment.

得益于 DNA 测序技术和生物信息学的进步，我们对微生物和微生物群落的了解比以往任何时候都多，过去三十年的工作揭示了地球上每个栖息地的微生物具有惊人的多样性，研究人员现在正试图将这种多样性联系起来。了解废水反应器和人类肠道等各种环境中的微生物（微生物组）开辟了新的应用，包括减轻人类疾病和修复污染场地。 尽管这场“微生物革命”前景广阔，但研究人员仍难以深入了解微生物组。单个环境样本中微生物物种的多样性可能超过 1,000 个，这是了解一个系统的生态的一个重大障碍。还含有数百万个不同的微生物基因，这个数量使人类基因组中的 20,000-25,000 个基因相形见绌。然而，最关键的限制因素是我们不知道是什么。当我们检查微生物群落时，以物种等自然分组为前提的方法不可避免地会错过数据中的重要模式，我们需要用微生物多样性的新表示来扩展我们的微生物组学工具箱。 我的研究计划涉及微生物组的多样性和进化，该提案包括两个互补的项目，这将提高我们解构和描述微生物群落的能力。首先，我们将开发新的生态模型，将单个基因视为物种并代表一个有机体。作为这些基因相互作用的整个生态系统，这种“基因生态学”模型将使我们能够将多样性、分散和竞争等传统概念纳入微生物基因组的研究中。基于随时间变化的协方差、多个栖息地的共现、相似的功能和生态作用以及传统的分类学相似性，这些新定义将产生数量惊人的候选单位，我们将开发新的方法来识别和解释候选单位。与特定的生态问题最相关。 微生物基因生态学将提供对微生物组中基因产物之间复杂相互作用的更好理解，而一组扩展的候选单元将帮助我们更好地评估微生物群落组成的变化，总之，这些技术将告诉我们微生物的哪些成员。当我们试图开发微生物解决方案来解决人类的一系列问题时，这些理解将至关重要。健康和环境。