The Pseudomonas putida group comprises strains with biotechnological and clinical relevance. P. alloputida was proposed as a new species and highlighted the misclassification of P. putida. Nevertheless, the population structure of P. alloputida remained unexplored. We retrieved 11,025 Pseudomonas genomes and used P. alloputida Kh7^T to delineate the species. The P. alloputida population structure comprises at least 7 clonal complexes (CCs). Clinical isolates are mainly found in CC4 and acquired resistance genes are present at low frequency in plasmids. Virulence profiles support the potential of CC7 members to outcompete other plant or human pathogens through a type VI secretion system. Finally, we found that horizontal gene transfer had an important role in shaping the ability of P. alloputida to bioremediate aromatic compounds such as toluene. Our results provide the grounds to understand P. alloputida genetic diversity and its potential for biotechnological applications.

恶臭假单胞菌组包括具有生物技术和临床相关性的菌株。P. alloputida被提出作为一个新物种，并突出了P. putida的错误分类。然而，P. alloputida的种群结构仍未被探索。我们检索了 11,025 个假单胞菌基因组，并使用P. alloputida Kh7 ^T来描绘该物种。P. alloputida种群结构至少包含 7 个克隆复合体 (CC)。临床分离株主要存在于 CC4 中，获得性耐药基因在质粒中的频率较低。毒力谱支持 CC7 成员通过 VI 型分泌系统战胜其他植物或人类病原体的潜力。最后，我们发现水平基因转移在塑造P. alloputida生物修复甲苯等芳香族化合物的能力方面具有重要作用。我们的结果为了解P. alloputida遗传多样性及其在生物技术应用中的潜力提供了基础。