Lu Wenjing, Zha Biqing, Lyu Jie, LingHu Chenxi, Chen Jing, Deng Sisi, Zhang Xiangling, Li Liang, Wang Guoqing
West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China.
Jiujiang Center for Disease Control and Prevention, Jiujiang, China.
Front Microbiol. 2024 Dec 16;15:1500886. doi: 10.3389/fmicb.2024.1500886. eCollection 2024.
Numerous studies have demonstrated that is closely associated with human health. These bacteria colonize the mucus layer of the gastrointestinal tract and utilize mucin as their sole source of carbon and nitrogen. spp. exhibit potential as probiotics under specific conditions. However, the gene accumulation curve derived from pan-genome analysis suggests that the genome of strains remains open. Consequently, current genome mining efforts are insufficient to fully capture the intraspecific and interspecific characteristics of , necessitating continuous exploration of the genomic and phenotypic diversity of new isolates.
Based on this finding, we sequenced, assembled, and functionally annotated the whole genomes of four new human isolates from our laboratory: AKK-HX001, AKK-HX002, AKK-HX003, and AKK-HX004.
Phylogenetic analysis revealed that all four isolates belonged to the AmII phylogroup, whereas the type strain DSM 22959 is classified within the AmI phylogroup. Moreover, 2,184 shared homologous genes were identified among the four isolates. Functional annotation using the COG, KEGG, and CAZy databases indicated that the functional genes of the four isolates were primarily associated with metabolism. Two antibiotic resistance genes were identified in AKK-HX001 and AKK-HX002, while three resistance genes were detected in AKK-HX003 and AKK-HX004. Additionally, each of the four isolates possessed two virulence genes and three pathogenicity genes, none of which were associated with pathogenicity. The prediction of mobile genetic elements indicated unequal distributions of GIs among the isolates, and a complete CRISPR system was identified in all isolates except AKK-HX003. Two annotated regions of secondary metabolite biosynthesis genes, both belonging to Terpene, were detected using the antiSMASH online tool.
These findings indicate that the four isolates, which belong to a phylogroup distinct from the model strain DSM 22959, exhibit lower genetic risk and may serve as potential probiotic resources for future research.
大量研究表明，[具体细菌名称未给出]与人类健康密切相关。这些细菌定殖于胃肠道的黏液层，并利用黏蛋白作为其唯一的碳源和氮源。[具体细菌名称未给出]菌在特定条件下展现出作为益生菌的潜力。然而，基于泛基因组分析得出的基因积累曲线表明，[具体细菌名称未给出]菌株的基因组仍未封闭。因此，目前的基因组挖掘工作不足以充分捕捉[具体细菌名称未给出]的种内和种间特征，需要持续探索新分离株的基因组和表型多样性。
基于这一发现，我们对实验室新分离的四株人类菌株AKK-HX001、AKK-HX002、AKK-HX003和AKK-HX004进行了全基因组测序、组装和功能注释。
系统发育分析表明，所有四株分离株均属于AmII系统发育组，而模式菌株DSM 22959属于AmI系统发育组。此外，在这四株分离株中鉴定出2184个共享的同源基因。使用COG、KEGG和CAZy数据库进行功能注释表明，这四株分离株的功能基因主要与代谢相关。在AKK-HX001和AKK-HX002中鉴定出两个抗生素抗性基因，而在AKK-HX003和AKK-HX004中检测到三个抗性基因。此外，这四株分离株各拥有两个毒力基因和三个致病基因，其中没有一个与致病性相关。移动遗传元件的预测表明，基因岛在分离株中的分布不均，并且在除AKK-HX003之外的所有分离株中均鉴定出一个完整的CRISPR系统。使用antiSMASH在线工具检测到两个注释的次生代谢物生物合成基因区域，均属于萜类。
这些发现表明这四株[具体细菌名称未给出]分离株属于与模式菌株DSM 22959不同的系统发育组，遗传风险较低，可能作为未来研究的潜在益生菌资源。
