Dimensions: Ordering the microbial world into natural genetic, ecological, and functional units

维度：将微生物世界划分为自然遗传、生态和功能单元

• 批准号: 1831730
• 负责人: Howard Ochman
• 金额: $ 199.4万
• 依托单位: University of Texas at Austin
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-09-01 至 2024-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1831730&HistoricalAwards=false
• 关键词: Dimensions; Ordering; microbial; world; into

The vast majority of our planet's biological diversity is microbial, and this diversity is being discovered at unprecedented rates due to advances in DNA sequencing technologies. Understanding the roles of these organisms, however, has been greatly hindered by our ignorance of the extent of microbial diversity, how it is generated, maintained, and shaped by evolution, and how it functions in the Earth's ecosystems. Understanding these aspects of the microbial world are fundamental to several questions critical to society, such as "Are emerging diseases new species, or variants of existing ones?", and "How will microbial populations respond to changing climates?". This project has the ambitious goals of developing methods that will for the first time allow all microbial species to be classified in a biologically meaningful way, and it will reveal the factors that give rise to new species. The research is a collaboration between four laboratories that have complementary scientific strengths in microbial biology, genome analysis, evolutionary genetics, and statistics. In addition to advancing scientists' fundamental understanding of microbes, the project will provide an important platform for training undergraduates, graduate students, and the postdoctoral scholars that will soon become independent scientists. This research program itself involves three major aims. The first major aim is to identify bacterial species under the framework provided by the Biological Species Concept (BSC), which defines species as genetically and reproductively isolated units. Applying this framework will unify the phylogenetic organization of bacteria with that of eukaryotes, and allow the researchers to determine the functional and ecological differences among species, and to quantify the rates and amounts of genetic exchange between them. The second major aim is to distinguish "ecotypes" that represent ecologically, functionally, or geographically isolated populations within species. This aim will be based on a genetic framework called "coalescence" that is well-established in eukaryotic phylogenetics. This work will both uncover new dimensions of microbial diversity and develop new statistical tools for other scientists to use. The third major aim is to determine how the process of bacterial speciation occurs and whether it mimics the patterns observed in eukaryotes. This aim will be accomplished by examining the patterns of gene exchange in the genomes of bacteria that have co-diversified with their host species (including humans), and the results will provide the first measurement of the amount of time required for the emergence of new bacterial species.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

我们星球上绝大多数的生物多样性是微生物，由于DNA测序技术的进步，这种多样性正以前所未有的速度被发现。然而，由于我们对微生物多样性的程度、微生物多样性是如何产生、维持和通过进化形成的，以及微生物多样性在地球生态系统中如何发挥作用的无知，我们对这些生物的作用的理解受到了极大的阻碍。了解微生物世界的这些方面对于解决几个对社会至关重要的问题至关重要，例如“新出现的疾病是新物种，还是现有物种的变体？以及“微生物种群将如何应对气候变化？".该项目的雄心勃勃的目标是开发方法，首次允许所有微生物物种以具有生物学意义的方式进行分类，并揭示产生新物种的因素。该研究是四个实验室之间的合作，这些实验室在微生物生物学，基因组分析，进化遗传学和统计学方面具有互补的科学优势。除了提高科学家对微生物的基本认识外，该项目还将为培养本科生、研究生和即将成为独立科学家的博士后学者提供一个重要平台。 这项研究计划本身涉及三个主要目标。第一个主要目标是在生物物种概念（BSC）提供的框架下识别细菌物种，该概念将物种定义为遗传和生殖隔离的单位。应用这一框架将统一细菌与真核生物的系统发育组织，并允许研究人员确定物种之间的功能和生态差异，并量化它们之间遗传交换的速率和数量。第二个主要目的是区分“生态型”，代表生态，功能或地理上孤立的种群内的物种。这一目标将基于在真核生物遗传学中已经确立的称为“聚结”的遗传框架。这项工作将揭示微生物多样性的新维度，并为其他科学家开发新的统计工具。第三个主要目标是确定细菌物种形成过程是如何发生的，以及它是否模仿在真核生物中观察到的模式。这一目标将通过研究与宿主物种共同多样化的细菌基因组中的基因交换模式来实现（包括人类），该奖项反映了NSF的法定使命，并被认为值得通过使用基金会的智力价值和更广泛的评估来支持。影响审查标准。

项目成果

Unexpected myriad of co-occurring viral strains and species in one of the most abundant and microdiverse viruses on Earth

• DOI: 10.1038/s41396-021-01150-2
• 发表时间: 2021-11-13
• 期刊: ISME JOURNAL
• 影响因子: 11
• 作者: Martinez-Hernandez, Francisco;Diop, Awa;Martinez-Garcia, Manuel
• 通讯作者: Martinez-Garcia, Manuel

Impact of homologous recombination on core genome phylogenies.

同源重组对核心基因组系统发育的影响。

• DOI: 10.21203/rs.3.rs-29898/v1
• 发表时间: 2020
• 期刊: BMC genomics
• 影响因子: 4.4
• 作者: Stott CM, Bobay LM