Collaborative Research: Deciphering the Genetic Diversity of Viruses through Gene Networks

合作研究：通过基因网络破译病毒的遗传多样性

• 批准号: 1661357
• 负责人: Catherine Putonti
• 金额: $ 67.63万
• 依托单位: Loyola University of Chicago
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-05-15 至 2022-04-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1661357&HistoricalAwards=false
• 关键词: Collaborative; Research; Deciphering; Genetic; Diversity

Bacteriophages are viruses that infect bacteria and can have a profound impact on bacterial populations. These viruses are the most abundant and diverse members of most ecosystems on Earth, having been found in every environment that supports life. The majority of the DNA sequences of newly isolated bacteriophage samples bears little or no resemblance to any sequences contained within current databases. This means that identifying new samples by looking for similar sequences is not an effective strategy. It is therefore crucial to find different approaches to characterize these viruses, which will then help is understand the critical roles that they have as members of microbial communities. This research will develop a new network-based approach for classifying viruses, thereby opening new avenues for exploring virus ecology as well as providing genomic data for evolutionary studies. This new approach will redefine how the genetic diversity of viruses is represented, making possible direct analyses of complex viral communities at higher resolution than is currently possible. Furthermore, the project will unite students from the computational and biological sciences, creating interdisciplinary teams able to carry out this research, with this training taking both in the classroom and laboratory.The project will develop a new graphical framework for the investigation of viral metagenomes, specifically aimed at putting novel viral sequences into a global context of viral genetic diversity. Because virus genomes are mosaics of genes acquired over time from multiple sources, a 'gene-centric' rather than a 'genome-centric' approach to classify the sequences in viromes is taken. In addition to capturing the combinatorial structure of virus genomes, this approach is robust to variation in genome and contig size that can arise from diverse datasets. Through the development of novel algorithms and metrics, evolutionary and ecological signals in the data will be integrated to inform the network's structure. The network will also be used to test hypotheses driven from the data, in particular the signals of viral host-range. For more information about the project visit the PI's lab website at http://www.putonti-lab.com.

噬菌体是感染细菌的病毒，可以对细菌种群产生深远的影响。这些病毒是地球上大多数生态系统中最丰富和最多样化的成员，在每一个支持生命的环境中都有发现。大多数新分离的噬菌体样品的DNA序列与当前数据库中包含的任何序列几乎没有相似性。这意味着通过寻找相似序列来识别新样本不是一种有效的策略。因此，找到不同的方法来表征这些病毒至关重要，这将有助于了解它们作为微生物群落成员的关键作用。这项研究将开发一种新的基于网络的病毒分类方法，从而为探索病毒生态学开辟新的途径，并为进化研究提供基因组数据。这种新方法将重新定义病毒遗传多样性的表现方式，从而可以以比目前更高的分辨率直接分析复杂的病毒群落。此外，该项目将联合来自计算科学和生物科学的学生，创建能够开展这项研究的跨学科团队，这种培训将在课堂和实验室进行。该项目将开发一个新的图形框架，用于研究病毒宏基因组，特别是旨在将新的病毒序列纳入病毒遗传多样性的全球背景下。因为病毒基因组是随时间从多个来源获得的基因的镶嵌体，所以采用"基因中心"而不是"基因组中心"的方法来对病毒组中的序列进行分类。除了捕获病毒基因组的组合结构之外，这种方法对于可能来自不同数据集的基因组和重叠群大小的变化是稳健的。通过开发新的算法和指标，数据中的进化和生态信号将被整合，以告知网络的结构。该网络还将用于测试由数据驱动的假设，特别是病毒宿主范围的信号。有关该项目的更多信息，请访问PI的实验室网站www.example.com。

项目成果

Complete Genome Sequence of a Pseudomonas aeruginosa Isolate from a Kidney Stone

• DOI: 10.1128/mra.01073-19
• 发表时间: 2019-09-01
• 期刊: MICROBIOLOGY RESOURCE ANNOUNCEMENTS
• 影响因子: 0.8
• 作者: Johnson, Genevieve;Stark, Nicole;Putonti, Catherine
• 通讯作者: Putonti, Catherine

Grindylow and Bassie: Characterization of Novel Escherichia Bacteriophages

Grindylow 和 Bassie：新型大肠杆菌噬菌体的表征

• 发表时间: 2018
• 期刊: Molecular Genetics of Bacteria and Phages Meeting
• 作者: Brassil, B;Putonti, C
• 通讯作者: Putonti, C

Corynebacterium phoceense, resident member of the urogenital microbiota?

• DOI: 10.1099/mic.0.001068
• 发表时间: 2021-07-01
• 期刊: MICROBIOLOGY-SGM
• 影响因子: 2.8
• 作者: Giannattasio-Ferraz, Silvia;Ene, Adriana;Putonti, Catherine
• 通讯作者: Putonti, Catherine

Characterization and spontaneous induction of urinary tract Streptococcus anginosus prophages

• DOI: 10.1099/jgv.0.001407
• 发表时间: 2020-01-01
• 期刊: JOURNAL OF GENERAL VIROLOGY
• 影响因子: 3.8
• 作者: Brassil, Bridget;Mores, Carine R.;Putonti, Catherine
• 通讯作者: Putonti, Catherine

Detecting viral genomes in the female urinary microbiome

• DOI: 10.1099/jgv.0.001097
• 发表时间: 2018-08-01
• 期刊: JOURNAL OF GENERAL VIROLOGY
• 影响因子: 3.8
• 作者: Garretto, Andrea;Thomas-White, Krystal;Putonti, Catherine
• 通讯作者: Putonti, Catherine