Meka Abu Feyisa, Bekele Gessesse Kebede, Abas Musin Kelel, Gemeda Mesfin Tafesse
Department of Biotechnology, Addis Ababa Science and Technology University, Addis Ababa, Ethiopia.
Department of Biology, Bule Hora University, Bule Hora, Ethiopia.
PLoS One. 2025 Mar 6;20(3):e0315536. doi: 10.1371/journal.pone.0315536. eCollection 2025.
Sof Umer Cave is an unexplored extreme environment that hosts novel microbes and potential genetic resources. Microbiomes from caves have been genetically adapted to produce various bioactive metabolites, allowing them to survive and tolerate harsh conditions. However, the biosynthesis-related gene cluster signatures in the microbiomes of Sof Umer Cave have not been explored. Therefore, high-throughput shotgun sequencing was used to explore biosynthesis-related gene clusters (BGCs) in the microbiomes of Sof Umer Cave. The GeneAll DNA Soil Mini Kit was used to extract high-molecular-weight DNA from homogenized samples, and the purified DNA was sequenced using a NovaSeq PE150. According to the Micro-RN database, the most common microbial genera in Sof Umer Cave are Protobacteria, Actinobacteria, Verrucomicrobiota, and Cyanobacteria. The biosynthesis-related gene clusters were annotated and classified, and the BGCs were predicted using antiSMASH and NAPDOS1. A total of 460 putative regions of BGCs encoding a wide range of secondary metabolites were identified, including RiPP (47.82%), terpene (19.57%), NRPS (13.04%), hybrid (2.18%), and other newly annotated (10.87%) compounds. Additionally, the NAPDOS pipeline identified a calcium-dependent antibiotic gene cluster from Streptomyces coelicolor, an actinomycin gene cluster from Streptomyces chrysomallus, and a bleomycin gene cluster from Streptomyces verticillus. These findings highlight the untapped biosynthetic potential of the Sof Umer Cave microbiome, as well as its potential for the discovery of natural products.
索夫·乌默尔洞穴是一个未被探索的极端环境，其中存在着新型微生物和潜在的遗传资源。洞穴中的微生物群落已经在基因上适应了产生各种生物活性代谢物，从而使它们能够在恶劣条件下生存和耐受。然而，索夫·乌默尔洞穴微生物群落中与生物合成相关的基因簇特征尚未得到探索。因此，采用高通量鸟枪法测序来探索索夫·乌默尔洞穴微生物群落中与生物合成相关的基因簇（BGCs）。使用GeneAll DNA土壤微量提取试剂盒从匀浆样品中提取高分子量DNA，并使用NovaSeq PE150对纯化后的DNA进行测序。根据Micro-RN数据库，索夫·乌默尔洞穴中最常见的微生物属是原核生物、放线菌、疣微菌门和蓝细菌。对与生物合成相关的基因簇进行了注释和分类，并使用antiSMASH和NAPDOS1预测了BGCs。总共鉴定出460个假定的BGC区域，编码范围广泛的次生代谢物，包括核糖体合成和翻译后修饰肽（RiPP，47.82%）、萜类化合物（19.57%）、非核糖体肽合成酶（NRPS，13.04%）、杂合型（2.18%）以及其他新注释的化合物（10.87%）。此外，NAPDOS管道从天蓝色链霉菌中鉴定出一个钙依赖性抗生素基因簇，从金色链霉菌中鉴定出一个放线菌素基因簇，从弗氏链霉菌中鉴定出一个博来霉素基因簇。这些发现突出了索夫·乌默尔洞穴微生物群落未被开发的生物合成潜力，以及其在天然产物发现方面的潜力。
