Nawaz Shahid, Skala Leigh, Amin Muhammad, Iruegas-Bocardo Fernanda, Samadi Arash, Zaman K H Ahammad Uz, Chang Jeff H, Sajid Imran, Mahmud Taifo
Institute of Microbiology and Molecular Genetics, University of the Punjab, Lahore, 54590, Pakistan.
Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR, 97333, USA.
Appl Biochem Biotechnol. 2025 Apr;197(4):2667-2680. doi: 10.1007/s12010-024-05158-0. Epub 2025 Jan 9.
Caves are a unique ecosystem that harbor diverse microorganisms, and provide a challenging environment to the dwelling microbial communities, which may boost gene expression and can lead to the production of inimitable bioactive natural products. In this study, we obtained 59 actinobacteria from four different caves located in Bahadurkhel, District Karak, Pakistan. On the basis of taxonomic characteristics, 30 isolates were selected and screened for secondary metabolites production and bioactivity profiling. The extracts of all the isolates exhibited promising antibacterial activity against several pathogenic bacteria, with the best outcome seen in the extract of isolate SNK 21. The metabolomic analysis of the extracts by LC-MS/MS-based molecular networking and whole genome sequencing (WGS) followed by antiSMASH analysis revealed the presence of diverse secondary metabolites and biosynthetic gene clusters (BGCs) in SNK 21. Purification of compounds by manual chromatography, HPLC, and characterization by NMR, HR-MS, led to the identification of the active compounds, actinomycin D and its isomer. In addition, metabolomic analysis and genome mining of morphologically distinct isolates, SNK 202 and SNK 329, also showed diverse secondary metabolites and BGCs, underscoring the potential of actinobacteria from undisturbed caves in Pakistan as a new source of bioactive compounds.
洞穴是一个独特的生态系统，其中蕴藏着多样的微生物，为栖息的微生物群落提供了具有挑战性的环境，这可能会促进基因表达，并导致产生独特的生物活性天然产物。在本研究中，我们从巴基斯坦卡拉奇县巴哈杜尔凯尔的四个不同洞穴中获得了59株放线菌。基于分类学特征，选择了30株分离株，并对其次级代谢产物生产和生物活性谱进行了筛选。所有分离株的提取物对几种病原菌均表现出有前景的抗菌活性，其中分离株SNK 21的提取物效果最佳。通过基于液相色谱-质谱/质谱的分子网络和全基因组测序（WGS）对提取物进行代谢组学分析，随后进行抗SMASH分析，结果显示SNK 21中存在多种次级代谢产物和生物合成基因簇（BGCs）。通过手动色谱法、高效液相色谱法对化合物进行纯化，并通过核磁共振、高分辨质谱进行表征，从而鉴定出活性化合物放线菌素D及其异构体。此外，对形态不同的分离株SNK 202和SNK 329进行代谢组学分析和基因组挖掘，也显示出多种次级代谢产物和BGCs，突出了巴基斯坦未受干扰洞穴中的放线菌作为生物活性化合物新来源的潜力。
