Population and evolutionary dynamics of recombining genes and alleles in bacteria

细菌重组基因和等位基因的种群和进化动力学

• 批准号: 10650790
• 负责人: Cheryl Marie P Andam
• 金额: $ 30.32万
• 依托单位: STATE UNIVERSITY OF NEW YORK AT ALBANY
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-08-09 至 2026-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10650790
• 关键词: Address; Alleles; Bacteria; Biological; Biology; Breeding; Cells; Clinical; Computational Biology; Creativeness; DNA; Disease; Ecology; Epidemiology; Evolution; Experimental Models; Fostering; Frequencies; Gene Combinations; Genetic; Genetic Recombination; Genome; Genomics; Goals; Health; Human; Immune system; Individual; Intervention; Knowledge; Microbe; Microbial Genetics; Microbiology; Mission; Modeling; National Institute of General Medical Sciences; Organism; Output; Pattern; Population; Population Process; Probability; Process; Public Health; Research; Resistance; Societies; Structure; Taxonomy; Variant; Virulence; Work; burden of illness; comparative; innovation; laboratory experiment; mathematical model; novel; offspring; pathogen; resistant strain; response; trait

PROJECT SUMMARY/ABSTRACT Species are conventionally defined as groups of individuals that breed with each other and produce fertile offspring, but not with those of other species (according to Ernst Mayr's Biological Species Concept). However, it is difficult to apply this eukaryotic definition of species to microbes because, even if they reproduce clonally, DNA may be acquired between strains and between species. Genetic recombination allows a bacterial cell to acquire novel traits through incorporation of DNA fragments from other organisms into its own genome. Recombination influences a myriad of evolutionary and population processes, including levels of standing diversity, niche expansion, spread of resistance and virulence determinants, and rapid adaptive changes in response to new or fluctuating environmental conditions. These processes are fundamental to questions critical to society and public health, such as whether an emerging disease is caused by a new species or variants of existing ones, what factors make a strain resistant or transmissible, and how a pathogen will respond to clinical interventions and host immune system. It is often assumed that all strains recombine at a uniform frequency and randomly across the entire species. However, recent work from the PI's lab show that recombination rates of strains of the same species vary along a continuum spanning several orders of magnitude, with a unique pattern of exchange for different strains and lineages. The causes and consequences of within-species variation in recombination is poorly understood, and therefore we still lack a coherent model for genome evolution that incorporates this variation. Filling in this gap in our knowledge of recombination has important ramifications for understanding species formation in microbes and the mechanisms that keep them separate once they begin to diverge. The goal of our proposed research is to elucidate how variation in recombination rates between strains impact population structure, genome evolution and speciation in microbes. Using a combination of comparative population genomics, laboratory experiments and mathematical modeling, we will answer the following questions: (1) To what extent does the probability of recombination influenced by the genetic distance and ecology of the parental strains? (2) How do different modes and genetic units of recombination vary across a species? (3) What are the evolutionary consequences of variable recombination rates in genome structure and divergence? Output from this research will help address the fundamental question in microbiology of whether species exist and if so, what processes keep them separate and distinct. The proposed research will also be a significant step forward to developing an evolution-based taxonomical framework and species boundaries for microbes. The results of the studies proposed in this application are expected to lead to other opportunities for fruitful cross-disciplinary research at the boundary of evolutionary biology, microbial genetics, computational biology and epidemiology.

项目概要/摘要 物种通常被定义为相互繁殖并产生后代的个体群体 有生育能力的后代，但不能与其他物种的后代（根据恩斯特·迈尔的生物物种概念）。 然而，很难将这种真核物种定义应用于微生物，因为即使它们能够繁殖 就克隆而言，DNA可以在菌株之间和物种之间获得。基因重组允许 细菌细胞通过将其他生物体的 DNA 片段整合到自己的细胞中来获得新的特征 基因组。重组影响着无数的进化和种群过程，包括 长期多样性、生态位扩展、耐药性和毒力决定因素的传播以及快速适应 因应新的或波动的环境条件而发生的变化。这些过程是基础 对社会和公共卫生至关重要的问题，例如新出现的疾病是否是由新的疾病引起的 现有菌株的物种或变种，哪些因素使菌株具有抗药性或可传播性，以及病原体如何 将对临床干预和宿主免疫系统做出反应。通常假设所有菌株在以下位置重组： 整个物种的频率一致且随机。然而，PI 实验室最近的工作表明 同一物种菌株的重组率沿着跨越几个数量级的连续体变化 大小，具有不同菌株和谱系的独特交换模式。其原因及 我们对种内重组变异的后果知之甚少，因此我们仍然缺乏 包含这种变异的基因组进化的连贯模型。填补了我们在这方面的知识空白 重组对于理解微生物的物种形成和 一旦它们开始分歧，就会有机制将它们分开。我们提出的研究的目标是 阐明菌株之间重组率的变化如何影响种群结构、基因组进化 和微生物的物种形成。结合比较群体基因组学、实验室实验 和数学建模，我们将回答以下问题：（1）概率在多大程度上 重组受亲本菌株的遗传距离和生态学影响吗？ (2) 有何不同 重组的模式和遗传单位因物种而异？ (3) 进化的后果是什么 基因组结构和分歧中可变重组率的影响？这项研究的成果将有助于 解决微生物学中的基本问题，即物种是否存在，如果存在，则保持哪些过程 它们是分开且不同的。拟议的研究也将是朝着开发 基于进化的微生物分类框架和物种边界。研究结果 本申请中提出的建议预计将为以下领域的富有成果的跨学科研究带来其他机会 进化生物学、微生物遗传学、计算生物学和流行病学的边界。

项目成果

Frequencies and characteristics of genome-wide recombination in Streptococcus agalactiae, Streptococcus pyogenes, and Streptococcus suis.

无乳链球菌、化脓链球菌和猪链球菌全基因组重组的频率和特征。

• 发表时间: 2022-01-27
• 影响因子: 4.6
• 作者: Lee, Isaiah Paolo A;Andam, Cheryl P
• 通讯作者: Andam, Cheryl P

Shared antibiotic resistance and virulence genes in Staphylococcus aureus from diverse animal hosts.

来自不同动物宿主的金黄色葡萄球菌具有共同的抗生素抗性和毒力基因。

• 发表时间: 2022-03-15
• 影响因子: 4.6
• 作者: Bruce, Spencer A;Smith, Joshua T;Mydosh, Jennifer L;Ball, John;Needle, David B;Gibson, Robert;Andam, Cheryl P
• 通讯作者: Andam, Cheryl P

Genome Evolution of Invasive Methicillin-Resistant Staphylococcus aureus in the Americas.

美洲侵袭性耐甲氧西林金黄色葡萄球菌的基因组进化。

• 发表时间: 2022-06-29
• 影响因子: 3.7
• 作者: Smith, Joshua T;Eckhardt, Elissa M;Hansel, Nicole B;Rahmani Eliato, Tahmineh;Martin, Isabella W;Andam, Cheryl P
• 通讯作者: Andam, Cheryl P

Prophage-encoded immune evasion factors are critical for Staphylococcus aureus host infection, switching, and adaptation.

原噬菌体编码的免疫逃避因子对于金黄色葡萄球菌宿主感染、转换和适应至关重要。

• 发表时间: 2022-11-09
• 作者: Chaguza, Chrispin;Smith, Joshua T;Bruce, Spencer A;Gibson, Robert;Martin, Isabella W;Andam, Cheryl P
• 通讯作者: Andam, Cheryl P

Population analysis of heavy metal and biocide resistance genes in Salmonella enterica from human clinical cases in New Hampshire, United States.

美国新罕布什尔州人类临床病例肠道沙门氏菌中重金属和杀菌剂抗性基因的群体分析。

• 发表时间: 2022
• 作者: Souza, Stephanie S R;Turcotte, Madison R;Li, Jinfeng;Zhang, Xinglu;Wolfe, Kristin L;Gao, Fengxiang;Benton, Christopher S;Andam, Cheryl P
• 通讯作者: Andam, Cheryl P