Streptomyces antimicrobicus sp. nov., a novel clay soil-derived actinobacterium producing antimicrobials against drug-resistant bacteria

A novel actinobacterium, designated strain SMC 277 T , was isolated from the clay soil in paddy field of Chonburi Province, Thailand, and characterized using polyphasic taxonomy. Strain SMC 277 T formed straight chains of nonmotile cylindrical spores with smooth surface developed on aerial mycelia. The typical chemotaxonomic properties of members of the genus Streptomyces were observed in strain SMC 277 T , e.g., cell wall peptidoglycan, whole cell sugars, major menaquinones, cellular fatty acids, and polar lipids. Chemotaxonomic data combined with mycelium and spore morphologies supported the assignment of strain SMC 277 T to the genus Streptomyces . The results of comparative analysis of the 16S rRNA gene sequences confirmed that strain SMC 277 T represented a member of the genus Streptomyces . Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SMC 277 T shared the highest sequence similarity with Streptomyces bambusae NBRC 110903 T (98.8%). Genome sequencing revealed a genome size of 6.55 Mbp and a digital G+C content of 73.4 mol%. In addition to the differences in phenotypic characteristics (morphology and physiology), values of ANI (ANIb and ANIm), AAI and dDDH between strain SMC 277 T and its closest relative S . bambusae NBRC 110903 T were 81.84, 86.77, 76.91 and 26.1%, respectively. Genome annotation and secondary metabolite gene cluster analysis predicted that SMC 277 T contained 35 biosynthetic gene clusters encoding diverse bioactive secondary metabolites. It is in agreement with observed antimicrobial activity against drug-resistant bacteria associated with nosocomial infections (methicillin-resistant Staphylococcus aureus , extended-spectrum β-lactamase producing Klebsiella pneumoniae , and multidrug-resistant Acinetobacter baumannii ). On the basis of these genotypic and phenotypic characteristics, strain SMC 277 T can be characterized to represent a novel species of the genus Streptomyces , for which the name Streptomyces antimicrobicus is proposed. The type strain is SMC 277 T (= TBRC 15568 T = NBRC 115422 T ).