Genome Insights into Kocuria sp. KH4, a Metallophilic Bacterium Harboring Multiple Biosynthetic Gene Clusters (BGCs)

The genus Kocuria includes Gram-positive and environmentally versatile bacteria, which are of biotechnological interest due to their ability to synthesize secondary metabolites. In this study, the genome of Kocuria sp. KH4, isolated from alkaline mine tailings (southeastern Mexico), was sequenced and analyzed to determine its taxonomic affiliation and explore its metabolic and adaptive potential. The assembled genome showed a size of 3.89 Mb, a GC content of 73.2%, and 3609 coding genes. Phylogenomic analyses and genomic relationship indices (ANI, AAI, and dDDH) confirmed that strain KH4 represents a novel genomospecies within the genus Kocuria. Functional analysis revealed broad metabolic diversity, with genes associated with the transport and metabolism of amino acids, carbohydrates, and inorganic ions. A total of 165 genes linked to metal resistance and homeostasis mechanisms were identified, including ABC-type transport systems and ATPases, as well as specific genes for Fe, Ni, Zn, Cu, As, and Hg. Forty-eight genomic islands were also identified, encoding a wide variety of functions and mobile genetic elements (MGEs). Furthermore, six biosynthetic gene clusters (BGCs) involved in the production of nonribosomal peptides, type III polyketides, terpenes, and siderophores were detected, suggesting a remarkable potential for the synthesis of bioactive compounds. Taken together, the results highlight this strain as a promising source of secondary metabolites with potential applications in environmental, pharmaceutical, and industrial biotechnology, underscoring the importance of Kocuria genomes as natural reservoirs of new biosynthetic pathways.