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.

项目总结/文摘

项目成果

Accessory Genome Dynamics of Local and Global Staphylococcus pseudintermedius Populations.

• DOI: 10.3389/fmicb.2022.798175
• 发表时间: 2022
• 期刊: Frontiers in microbiology
• 影响因子: 5.2
• 作者: Bruce SA;Smith JT;Mydosh JL;Ball J;Needle DB;Gibson R;Andam CP
• 通讯作者: Andam CP

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

• DOI: 10.3389/fmicb.2022.983083
• 发表时间: 2022
• 期刊: Frontiers in microbiology
• 影响因子: 5.2

Genome characteristics of clinical Salmonella enterica population from a state public health laboratory, New Hampshire, USA, 2017-2020.

• DOI: 10.1186/s12864-022-08769-1
• 发表时间: 2022-07-23
• 期刊: BMC GENOMICS
• 影响因子: 4.4
• 作者: Turcotte, Madison R.;Smith, Joshua T.;Li, Jinfeng;Zhang, Xinglu;Wolfe, Kristin L.;Gao, Fengxiang;Benton, Christopher S.;Andam, Cheryl P.
• 通讯作者: Andam, Cheryl P.

Extensive Horizontal Gene Transfer within and between Species of Coagulase-Negative Staphylococcus.

• DOI: 10.1093/gbe/evab206
• 发表时间: 2021-09-01
• 期刊: Genome biology and evolution
• 影响因子: 3.3
• 作者: Smith JT;Andam CP
• 通讯作者: Andam CP

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

• DOI: 10.1038/s41598-022-08230-z
• 发表时间: 2022-03-15
• 期刊: Scientific reports
• 影响因子: 4.6
• 作者: Bruce SA;Smith JT;Mydosh JL;Ball J;Needle DB;Gibson R;Andam CP
• 通讯作者: Andam CP