Taxonomic Positions of a Nyuzenamide-Producer and Its Closely Related Strains.

sp. N11-34 is a producer of bicyclic peptides named nyuzenamides A and B. We elucidated its taxonomic position and surveyed its nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) gene clusters by whole genome analysis. sp. N11-34 showed 16S rRNA gene sequence similarities of 99.9% and 99.8% to NBRC 13472 and NRRL B-1478, respectively. Although these members formed a clade in a phylogenetic tree based on 16S rRNA gene sequences, the clade split into two closely related subclades in multilocus sequence analysis (MLSA). One included sp. N11-34, NRRL B-1478, NBRC 100766, NBRC 16556 and TP-A0867 and the other comprised NBRC 13472 and NBRC 12859. These phylogenetic relationships were supported by phylogenomic analysis. Although sp. N11-34 was classified to at the species level based on MLSA evolutionary distances and DNA-DNA relatedness, these distances and relatedness of members between the two subclades were comparatively far (0.004-0.006) and low (75.4-76.4%), respectively. sp. N11-34 possessed six NRPS, seven PKS and four hybrid PKS/NRPS gene clusters in the genome. Among the seventeen, ten were identified to be biosynthetic gene clusters (BGCs) of nyuzenamide, echoside, coelichelin, geldanamycin, mediomycin, nigericin, azalomycin, spore pigment, alchivemycin and totopotensamide, whereas the remaining seven were orphan in our bioinformatic analysis. All seventeen are conserved in NBRC 100766, NBRC 16556 and TP-A0867. In contrast, NBRC 13472 and NBRC 12859 lacked the BGCs of alchivemycin, totopotensamide, a nonribosomal peptide and a hybrid polyketide/nonribosomal peptide compound. This difference was in a good accordance with the abovementioned phylogenetic relationship. Based on phenotypic differences in addition to phylogenetic relationship, DNA-DNA relatedness and BGCs, strains of should be reclassified to two subspecies: subsp. and a new subspecies, for which we proposed subsp. subsp. nov. The type strain is NBRC 100766 (=ATCC 43692 = DSM 41460 = INMI 32 = JCM 9093 = NRRL B-16376 = VKM Ac-312). was classified in this subspecies.