Centre for Chemical Biology, Universiti Sains Malaysia, Penang 11900, Malaysia.
Int J Mol Sci. 2022 Aug 26;23(17):9712. doi: 10.3390/ijms23179712.
The genus is known for its ecophysiological versatility encompassing free-living, symbiotic, and pathogenic lifestyles. sp. CCB-ST2H9 was isolated from estuarine sediment collected at Matang Mangrove, Malaysia. In this study, the genome of CCB-ST2H9 was sequenced, and the pan-genome of 37 strains was analysed. Phylogeny based on core genes showed that CCB-ST2H9 clustered with , forming a distinct clade with , , and . The core genome of was conserved in housekeeping functions, while the flexible genome was well represented by environmental genes related to energy production and carbohydrate metabolism. Genomic metrics including 16S rRNA sequence similarity, average nucleotide identity, and digital DNA-DNA hybridization values were below the cut-off for species delineation, implying that CCB-ST2H9 potentially represents a new species. Genome mining revealed that biosynthetic gene clusters (BGCs) involved in producing antimicrobial compounds such as holomycin in CCB-ST2H9 could contribute to the antagonistic potential. Furthermore, the EtOAc extract from the culture broth of CCB-ST2H9 exhibited antagonistic activity against spp. Intriguingly, clustering based on BGCs profiles grouped , , , , and CCB-ST2H9 together in the heatmap by the presence of a large number of BGCs. These BGCs-rich strains represent great potential for bioactive secondary metabolites production and sources for novel compounds.
该属以其包含自由生活、共生和致病生活方式的生态生理多功能性而闻名。CCB-ST2H9 是从马来西亚马塘红树林采集的河口沉积物中分离出来的。在这项研究中，对 CCB-ST2H9 的基因组进行了测序，并对 37 株菌的泛基因组进行了分析。基于核心基因的系统发育树表明，CCB-ST2H9 与 聚类，与 、 、 形成一个独特的分支。的核心基因组在管家功能中保守，而与能量产生和碳水化合物代谢相关的环境基因则很好地代表了可变形基因组。包括 16S rRNA 序列相似性、平均核苷酸同一性和数字 DNA-DNA 杂交值在内的基因组指标均低于物种划分的截止值，这表明 CCB-ST2H9 可能代表一个新的物种。基因组挖掘显示，参与产生抗菌化合物的生物合成基因簇（BGCs），如 CCB-ST2H9 中的 holomycin，可能有助于其拮抗潜力。此外，CCB-ST2H9 发酵液的 EtOAc 提取物对 种表现出拮抗活性。有趣的是，基于 BGCs 图谱的聚类将 、 、 、 以及 CCB-ST2H9 聚集在一起，通过存在大量 BGCs 在热图中分组。这些 BGCs 丰富的 菌株代表了生物活性次生代谢产物产生的巨大潜力，也是新型化合物的来源。
