Unraveling the Genomic Diversity of the Pseudomonas putida Group: Exploring Taxonomy, Core Pangenome, and Antibiotic Resistance Mechanisms.

IF 10.1 2区 生物学 Q1 MICROBIOLOGY FEMS microbiology reviews Pub Date : 2024-10-10 DOI:10.1093/femsre/fuae025
Zulema Udaondo, Juan Luis Ramos, Kaleb Abram
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Abstract

The genus Pseudomonas is characterized by its rich genetic diversity, with over 300 species been validly recognized. This reflects significant progress made through sequencing and computational methods. Pseudomonas putida group comprises highly adaptable species that thrive in diverse environments and play various ecological roles, from promoting plant growth to being pathogenic in immunocompromised individuals. By leveraging the GRUMPS computational pipeline, we scrutinized 26363 genomes labeled as Pseudomonas in NCBI GenBank, categorizing all Pseudomonas spp. genomes into 435 distinct species-level clusters or cliques. We identified 224 strains deposited under the taxonomic identifier "Pseudomonas putida" distributed within 31 of these species-level clusters, challenging prior classifications. Nine of these 31 cliques contained at least six genomes labeled as "Pseudomonas putida" and were analyzed in depth, particularly clique_1 (P. alloputida) and clique_2 (P. putida). Pangenomic analysis of a set of 413 P. putida group strains revealed over 2.2 million proteins and more than 77000 distinct protein families. The core genome of these 413 strains includes 2226 protein families involved in essential biological processes. Intraspecific genetic homogeneity was observed within each clique, each possessing a distinct genomic identity. These cliques exhibit distinct core genes and diverse subgroups, reflecting adaptation to specific environments. Contrary to traditional views, nosocomial infections by P. alloputida, P. putida, and P. monteilii have been reported, with strains showing varied antibiotic resistance profiles due to diverse mechanisms. This review enhances the taxonomic understanding of key P. putida group species using advanced population genomics approaches and provides a comprehensive understanding of their genetic diversity, ecological roles, interactions, and potential applications.

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揭示假单胞菌群的基因组多样性:探索分类、核心庞基因组和抗生素耐药性机制。
假单胞菌属的特点是遗传多样性丰富,目前已确认的有效物种超过 300 种。这反映了通过测序和计算方法所取得的重大进展。假单胞菌群由适应性很强的物种组成,它们在不同的环境中茁壮成长,扮演着各种生态角色,从促进植物生长到对免疫力低下的个体具有致病性。通过利用 GRUMPS 计算管道,我们仔细研究了 NCBI GenBank 中标注为假单胞菌的 26363 个基因组,将所有假单胞菌属基因组分为 435 个不同的物种级簇或群。我们发现了 224 株以分类标识符 "Pseudomonas putida "保存的菌株,它们分布在其中 31 个物种级群组中,这对之前的分类提出了挑战。在这 31 个聚类中,有 9 个聚类包含至少 6 个标记为 "Pseudomonas putida "的基因组,我们对这 9 个聚类进行了深入分析,特别是 clique_1(P. alloputida)和 clique_2(P. putida)。对一组 413 株假丝酵母菌群的庞基因组分析发现了 220 多万个蛋白质和 77000 多个不同的蛋白质家族。这 413 株菌株的核心基因组包括 2226 个参与重要生物过程的蛋白质家族。在每个小群中都观察到了种内遗传同质性,每个小群都拥有独特的基因组特征。这些小群显示出不同的核心基因和多样化的亚群,反映出对特定环境的适应。与传统观点不同的是,有报道称 P.alloputida、P.putida 和 P. monteilii 造成了院内感染,其菌株因机制不同而表现出不同的抗生素耐药性。这篇综述利用先进的群体基因组学方法加强了对普氏拟杆菌群主要物种的分类学认识,并提供了对其遗传多样性、生态作用、相互作用和潜在应用的全面了解。
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来源期刊
FEMS microbiology reviews
FEMS microbiology reviews 生物-微生物学
CiteScore
17.50
自引率
0.90%
发文量
45
审稿时长
6-12 weeks
期刊介绍: Title: FEMS Microbiology Reviews Journal Focus: Publishes reviews covering all aspects of microbiology not recently surveyed Reviews topics of current interest Provides comprehensive, critical, and authoritative coverage Offers new perspectives and critical, detailed discussions of significant trends May contain speculative and selective elements Aimed at both specialists and general readers Reviews should be framed within the context of general microbiology and biology Submission Criteria: Manuscripts should not be unevaluated compilations of literature Lectures delivered at symposia must review the related field to be acceptable
期刊最新文献
The biochemical mechanisms of plastic biodegradation. Assembly of functional microbial ecosystems: from molecular circuits to communities. Unraveling the Genomic Diversity of the Pseudomonas putida Group: Exploring Taxonomy, Core Pangenome, and Antibiotic Resistance Mechanisms. Methods for studying microbial acid stress responses: from molecules to populations. The rise and future of CRISPR-based approaches for high-throughput genomics.
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