Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, United States.
Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, c/Profesor Albareda n° 1, 18008 Granada, Spain.
FEMS Microbiol Rev. 2024 Nov 23;48(6). doi: 10.1093/femsre/fuae025.
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 26 363 genomes labeled as Pseudomonas in the 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 analysed 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 77 000 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.
假单胞菌属的特点是其丰富的遗传多样性，目前已有效确认了 300 多种物种。这反映了通过测序和计算方法取得的重大进展。恶臭假单胞菌群包括高度适应性的物种，它们在各种环境中茁壮成长，发挥着多种生态作用，从促进植物生长到在免疫功能低下的个体中成为病原体。通过利用 GRUMPS 计算管道，我们仔细研究了 NCBI GenBank 中标记为假单胞菌的 26363 个基因组，将所有假单胞菌属的基因组分为 435 个不同的种水平聚类或集团。我们确定了 224 株以分类标识符“恶臭假单胞菌”保存的菌株，分布在这 31 个种水平聚类中的 31 个聚类中，这对先前的分类提出了挑战。这 31 个聚类中的 9 个包含至少 6 个标记为“恶臭假单胞菌”的基因组，并进行了深入分析，特别是聚类 1（P. alloputida）和聚类 2（P. putida）。一组 413 株假单胞菌属群体菌株的全基因组分析揭示了超过 220 万个蛋白质和超过 77000 个不同的蛋白质家族。这 413 株菌的核心基因组包括 2226 个参与基本生物过程的蛋白质家族。在每个聚类内观察到种内遗传同质性，每个聚类都具有独特的基因组特征。这些聚类表现出不同的核心基因和多样化的亚群，反映了对特定环境的适应。与传统观点相反，已报道了恶臭假单胞菌、铜绿假单胞菌和蒙特利假单胞菌引起的医院感染，由于不同的机制，这些菌株显示出不同的抗生素耐药谱。本综述利用先进的群体基因组学方法增强了对关键假单胞菌属群体物种的分类理解，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。
