Ochrobactrum genus is comprised of soil-dwelling Gram-negative bacteria mainly reported for bioremediation of toxic compounds. Since last few years, mainly two species of this genus, O. intermedium and O. anthropi were documented for causing infections mostly in the immunocompromised patients. Despite such ubiquitous presence, study of adaptation in various niches is still lacking. Thus, to gain insights into the niche adaptation strategies, pan-genome analysis was carried out by comparing 67 genome sequences belonging to Ochrobactrum species. Pan-genome analysis revealed it is an open pan-genome indicative of the continuously evolving nature of the genus. The presence/absence of gene clusters also illustrated the unique presence of antibiotic efflux transporter genes and type IV secretion system genes in the clinical strains while the genes of solvent resistance and exporter pumps in the environmental strains. A phylogenomic investigation based on 75 core genes depicted better and robust phylogenetic resolution and topology than the 16S rRNA gene. To support the pan-genome analysis, individual genomes were also investigated for the mobile genetic elements (MGE), antibiotic resistance genes (ARG), metal resistance genes (MRG) and virulence factors (VF). The analysis revealed the presence of MGE, ARG, and MRG in all the strains which play an important role in the species evolution which is in agreement with the pan-genome analysis. The average nucleotide identity (ANI) based on the genetic relatedness between the Ochrobactrum species indicated a distinction between individual species. Interestingly, the ANI tool was able to classify the Ochrobactrum genomes to the species level which were assigned till the genus level on the NCBI database.

中文翻译：

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来自临床和环境起源的 Ochrobactrum 物种的泛基因组学揭示了不同的种群和可能的联系。

Ochrobactrum 属由居住在土壤中的革兰氏阴性细菌组成，主要报道用于有毒化合物的生物修复。自最近几年以来，主要是该属的两个物种 O. intermedium 和 O. anthropi 被记录为主要在免疫功能低下的患者中引起感染。尽管存在这种无处不在的存在，但仍然缺乏对各种生态位适应性的研究。因此，为了深入了解生态位适应策略，通过比较属于 Ochrobactrum 物种的 67 个基因组序列进行了泛基因组分析。泛基因组分析表明它是一个开放的泛基因组，表明该属的不断进化的性质。基因簇的存在/不存在也说明了临床菌株中抗生素外排转运蛋白基因和IV型分泌系统基因的独特存在，而环境菌株中的耐溶剂性和出口泵基因。基于 75 个核心基因的系统发育研究描绘了比 16S rRNA 基因更好和稳健的系统发育分辨率和拓扑结构。为了支持泛基因组分析，还研究了个体基因组的移动遗传元件 (MGE)、抗生素抗性基因 (ARG)、金属抗性基因 (MRG) 和毒力因子 (VF)。分析揭示了在物种进化中起重要作用的所有菌株中均存在MGE、ARG和MRG，这与泛基因组分析一致。基于 Ochrobactrum 物种之间遗传相关性的平均核苷酸同一性 (ANI) 表明个体物种之间存在差异。有趣的是，ANI 工具能够将 Ochrobactrum 基因组分类到物种级别，这些级别被分配到 NCBI 数据库中的属级别。