Lema Niguse Kelile, Gemeda Mesfin Tafesse, Woldesemayat Adugna Abdi
Department of Biotechnology, Arba Minch University, Arba Minch, Ethiopia.
Department of Biotechnology, College of Natural and Applied Sciences, Addis Ababa Science and Technology University, Addis Ababa, Ethiopia.
Sci Rep. 2025 Jul 15;15(1):25500. doi: 10.1038/s41598-025-03467-w.
Hospital and pharmaceutical industry wastes harbor a diverse microbial community influenced by their complex chemical composition, including antibiotic-rich compounds originating from soil microorganisms. This study employs a shotgun metagenomic approach to comprehensively characterize the microbial composition of hospital and Pharmaceutical industry wastes for the first time in Ethiopia. Metagenomic DNA was extracted and used to construct a whole-genome shotgun library, which was subsequently sequenced using the Illumina HiSeq1500 platform. Taxonomic analysis revealed that bacteria were the predominant domain across all samples, followed by eukaryotes and archaea. Among the bacterial phyla, Pseudomonadota was the most prevalent in both hospital and pharmaceutical waste samples. At the genus level, Pseudomonas and Pedobacter were the most abundant taxa, followed by Flavobacterium and Streptomyces. Notably, Streptomyces exhibited higher-than-expected abundance in the waste metagenome, suggesting a potential adaptive response to environmental stressors. Across all samples, Pedobacter and Pseudomonas were consistently the most dominant bacterial genera. Functional analysis using gene ontology (GO) annotations highlighted the predominance of metabolic and biosynthetic processes. Further investigation revealed an enrichment of ATP-binding cassette (ABC) transporter protein families and winged-helix protein domains, both of which are linked to antibiotic resistance, metabolite translocation, and antibiotic biosynthesis regulation. KEGG pathway analysis identified key biosynthetic pathways, including terpenoid and polyketide biosynthesis, as well as beta-lactam antibiotic production. Additionally, antiSMASH analysis detected multiple biosynthetic gene clusters (BGCs), including those encoding terpenes, bacteriocins, and non-ribosomal peptide synthetases. Overall, this study underscores the adaptive potential of microorganisms inhabiting industrial waste environments, highlighting their genomic capacity to produce bioactive secondary metabolites in response to toxic compounds. These findings provide valuable insights into microbial resilience and the potential for biotechnological applications in bioremediation and drug discovery.
医院和制药行业废弃物中蕴藏着多样的微生物群落，其受复杂化学组成的影响，包括源自土壤微生物的富含抗生素的化合物。本研究首次在埃塞俄比亚采用鸟枪法宏基因组学方法全面表征医院和制药行业废弃物的微生物组成。提取宏基因组DNA并用于构建全基因组鸟枪文库，随后使用Illumina HiSeq1500平台进行测序。分类学分析表明，细菌是所有样本中的主要领域，其次是真核生物和古细菌。在细菌门中，假单胞菌门在医院和制药废弃物样本中最为普遍。在属水平上，假单胞菌属和 Pedobacter 属是最丰富的分类群，其次是黄杆菌属和链霉菌属。值得注意的是，链霉菌在废弃物宏基因组中的丰度高于预期，表明其对环境压力源可能存在适应性反应。在所有样本中，Pedobacter 属和假单胞菌属始终是最主要的细菌属。使用基因本体（GO）注释进行的功能分析突出了代谢和生物合成过程的优势。进一步研究发现ATP结合盒（ABC）转运蛋白家族和翼状螺旋蛋白结构域富集，这两者都与抗生素抗性、代谢物转运和抗生素生物合成调节有关。KEGG通路分析确定了关键的生物合成途径，包括萜类和聚酮类生物合成，以及β-内酰胺抗生素的生产。此外，antiSMASH分析检测到多个生物合成基因簇（BGC），包括那些编码萜类、细菌素和非核糖体肽合成酶的基因簇。总体而言，本研究强调了栖息在工业废弃物环境中的微生物的适应潜力，突出了它们响应有毒化合物产生生物活性次生代谢物的基因组能力。这些发现为微生物的恢复力以及在生物修复和药物发现中的生物技术应用潜力提供了有价值的见解。
