CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
University of Chinese Academy of Sciences, Beijing, 100049, China.
Nat Commun. 2024 Sep 15;15(1):8084. doi: 10.1038/s41467-024-51864-y.
Virulence factor genes (VFGs) play pivotal roles in bacterial infections and have been identified within the human gut microbiota. However, their involvement in chronic diseases remains poorly understood. Here, we establish an expanded VFG database (VFDB 2.0) consisting of 62,332 nonredundant orthologues and alleles of VFGs using species-specific average nucleotide identity ( https://github.com/Wanting-Dong/MetaVF_toolkit/tree/main/databases ). We further develop the MetaVF toolkit, facilitating the precise identification of pathobiont-carried VFGs at the species level. A thorough characterization of VFGs for 5452 commensal isolates from healthy individuals reveals that only 11 of 301 species harbour these factors. Further analyses of VFGs within the gut microbiomes of nine chronic diseases reveal both common and disease-specific VFG features. Notably, in type 2 diabetes patients, long HiFi sequencing confirms that shared VF features are carried by pathobiont strains of Escherichia coli and Klebsiella pneumoniae. These findings underscore the critical importance of identifying and understanding VFGs in microbiome-associated diseases.
毒力因子基因 (VFGs) 在细菌感染中发挥着关键作用，并已在人类肠道微生物群中被发现。然而，它们在慢性疾病中的作用仍知之甚少。在这里，我们使用物种特异性平均核苷酸同一性（https://github.com/Wanting-Dong/MetaVF_toolkit/tree/main/databases）建立了一个扩展的 VFG 数据库 (VFDB 2.0)，其中包含 62332 个非冗余的 VFG 直系同源物和等位基因。我们进一步开发了 MetaVF 工具包，以促进在物种水平上精确识别病原菌携带的 VFG。对 5452 个来自健康个体的共生体分离物的 VFG 进行了全面表征，结果表明只有 301 个物种中的 11 个携带这些因子。对 9 种慢性疾病的肠道微生物组中的 VFG 进行进一步分析揭示了共同和疾病特异性的 VFG 特征。值得注意的是，在 2 型糖尿病患者中，长 HiFi 测序证实了共享的 VF 特征由大肠杆菌和肺炎克雷伯菌的病原菌菌株携带。这些发现强调了在与微生物组相关的疾病中识别和理解 VFG 的至关重要性。
