Secondary metabolite biosynthetic gene clusters and microbial diversity as predicted by shotgun metagenomic sequencing approach in hospitals and pharmaceutical industry wastes.

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.