Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Kunming, China.
Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Center for Disease Control and Prevention, Kunming, China.
PLoS One. 2020 Feb 21;15(2):e0229125. doi: 10.1371/journal.pone.0229125. eCollection 2020.
Proteus spp. are commensal gastrointestinal bacteria in many hosts, but information regarding the mutual relationships between these bacteria and their hosts is limited. The tree shrew is an alternative laboratory animal widely used for human disease research. However, little is known about the relationship between Proteus spp. and tree shrews. In this study, the complete genome sequencing method was used to analyse the characteristics of Proteus spp. isolated from tree shrews, and comparative genomic analysis was performed to reveal their relationships. The results showed that 36 Proteus spp. bacteria were isolated, including 34 Proteus mirabilis strains and two Proteus vulgaris strains. The effective rate of sequencing was 93.53%±2.73%, with an average GC content of 39.94%±0.25%. Briefly, 3682.89±90.37, 2771.36±36.01 and 2832.06±42.49 genes were annotated in the NCBI non-redundant nucleotide database (NR), SwissProt database and KEGG database, respectively. The high proportions of macrolide-, vancomycin-, bacitracin-, and tetracycline-resistance profiles of the strains were annotated in the Antibiotic Resistance Genes Database (ARDB). Flagella, lipooligosaccharides, type 1 fimbriae and P fimbriae were the most abundantly annotated virulence factors in the Virulence Factor Database (VFDB). SNP variants indicated high proportions of base transitions (Ts), homozygous mutations (Hom) and non-synonymous mutations (Non-Syn) in Proteus spp. (P<0.05). Phylogenetic analysis of Proteus spp. and other references revealed high genetic diversity for strains isolated from tree shrews, and host specificity of Proteus spp. bacteria was not found. Overall, this study provided important information on characteristics of genome for Proteus spp. isolated from tree shrews.
变形杆菌属是许多宿主胃肠道内的共生细菌，但有关这些细菌与其宿主之间相互关系的信息有限。树鼩是一种广泛用于人类疾病研究的替代实验动物。然而，对于变形杆菌属与树鼩之间的关系知之甚少。在本研究中，采用全基因组测序方法分析了从树鼩中分离得到的变形杆菌属的特征，并进行了比较基因组分析以揭示它们之间的关系。结果表明，共分离得到 36 株变形杆菌属细菌，其中包括 34 株奇异变形杆菌和 2 株普通变形杆菌。测序有效率为 93.53%±2.73%，平均 GC 含量为 39.94%±0.25%。简而言之，在 NCBI 非冗余核苷酸数据库（NR）、SwissProt 数据库和 KEGG 数据库中分别注释了 3682.89±90.37、2771.36±36.01 和 2832.06±42.49 个基因。菌株对抗生素耐药基因数据库（ARDB）中各种抗生素的耐药谱分析表明，大环内酯类、万古霉素类、杆菌肽类和四环素类药物的耐药率较高。鞭毛、脂寡糖、I 型菌毛和 P 菌毛是在毒力因子数据库（VFDB）中注释最多的毒力因子。单核苷酸多态性（SNP）变异表明，变形杆菌属的碱基转换（Ts）、纯合突变（Hom）和非同义突变（Non-Syn）比例较高（P<0.05）。变形杆菌属与其他参考序列的系统发育分析显示，从树鼩中分离得到的菌株具有很高的遗传多样性，并未发现变形杆菌属细菌具有宿主特异性。总的来说，本研究为从树鼩中分离得到的变形杆菌属的基因组特征提供了重要信息。
