Emended descriptions of Streptomyces javensis and Streptomyces rhizosphaericus based on reclassifications of Streptomyces yogyakartensis, Streptomyces cangkringensis, and Streptomyces indonesiensis

Although some <i>Streptomyces</i> species share identical 16S rRNA gene sequences, their taxonomic relationships have not been adequately re-examined. Type strains of <i>Streptomyces javensis</i>, <i>Streptomyces yogyakartensis</i> and <i>Streptomyces violaceusniger</i> share the same 16S rRNA gene sequence. This study aimed to determine whether <i>S. javensis</i>, <i>S. yogyakartensis</i> and <i>S. violaceusniger</i> represent the same taxon using molecular and genome-based methods. Digital DNA-DNA hybridization revealed a relatedness of 89.4% between <i>S. javensis</i> JCM 11446^T and <i>S. yogyakartensis</i> JCM 11448^T, whereas the values for <i>S. violaceusniger</i> NBRC 13459^T to <i>S. javensis</i> JCM 11446^T and <i>S. yogyakartensis</i> JCM 11448^T were 53.7% and 55.1%, respectively. The type strains of <i>S. javensis</i> and <i>S. yogyakartensis</i> formed an independent clade in the phylogenomic tree, displaying similar phenotypes and sharing the same type I polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) gene clusters. Accordingly, <i>S. yogyakartensis</i> was reclassified as a later heterotypic synonym of <i>S. javensis</i>. Furthermore, the phylogenomic tree suggested that <i>Streptomyces rhizosphaericus</i> JCM 11447^T, <i>Streptomyces cangkringensis</i> DSM 41769^T and <i>Streptomyces indonesiensis</i> DSM 41759^T may be synonymous. DNA-DNA relatedness among them ranged 97.1-98.4%. Additionally, these type strains showed similar phenotypes, and most of their type I PKS and NRPS gene clusters were conserved. Based on these results, <i>S. cangkringensis</i> and <i>S. indonesiensis</i> were reclassified as heterotypic synonyms of <i>S. rhizosphaericus</i>. Descriptions of <i>S. javensis</i> and <i>S. rhizosphaericus</i> were emended according to the reclassifications.