Unveiling the genomic secrets of Micrococcus luteus through a comprehensive comparative genomics approach

The central motivation of this study was to analyze the unknown genomic facts of the ubiquitously distributed bacterium Micrococcus luteus using in silico comparative genomic analysis. A total of 100 contamination-free genomes were retrieved from the National Center for Biotechnology Information (NCBI). Among them, 12 strains from six different isolation sources were selected based on their ANI (average nucleotide identity) values to explore their niche-specific adaptation. Prokka annotation revealed that their total genome size ranged from 2.4 to 2.8 Mb, with plant-growth-promoting and heavy-metal resistance genes prevalent across the strains. There were tryptophan (precursor of indole acetic acid) biosynthesizing genes and aes family proteins, indicating its plant-growth promoting traits. Rapid annotation subsystem technology-based functional annotation also detected arsenic resistance (arsC and arsB), mercury resistance (merA, merB, and merR), and copper homeostasis (copZ and copD) genes. In-depth accessory genomic analysis revealed attributes such as genomic islands, prophage genomes, metal resistance, hypothetical proteins, insertion sequences (insertion sequence elements), and transposase. IslandViewer 4 identified 21-37 GIs which occupied up to 17% of the total genome. The presence of multiple IS elements was an intrinsic factor of this genome. The number ranged from 28 to 76 under 13 different families, with IS256 the most frequent element. PHASTER analysis identified PHAGE_Paenib_Tripp_NC_028930 as the most dominant prophage among strains with similar GC adaptation. Functional annotation identified 15,444 KEGG orthologs and 6,022 Pfam domains. Comprehensive Antibiotic Resistance Database suggested the antibiotic sensitivity of the species. Finally, despite the prevalent occurrence of M. luteus, it is still not multi-drug-resistant and can be applied in heavy-metal-contaminated agricultural field for plant growth promotion.