Streptomyces mitragynae sp. nov., isolated from Mitragyna speciosa leaves in Thailand, with antimicrobial activity and secondary metabolite profiling

Two novel endophytic actinomycete strains, NRAIS3^T and NRAIS4, belonging to the genus <i>Streptomyces</i>, were isolated from <i>Mitragyna speciosa</i> leaves. Their taxonomic status was determined using a polyphasic approach. Both strains grew at temperatures ranging from 25 to 37 °C and at pH values between 6 and 10. Strain NRAIS3ᵀ tolerated up to 5% (w/v) NaCl, whereas strain NRAIS4 tolerated up to 7% (w/v) NaCl. Both strains contained <i>ll</i>-diaminopimelic acid in their cell-wall peptidoglycan, and their whole-cell hydrolysates contained ribose and glucose. The predominant cellular fatty acids were <i>anteiso</i>-C_15:0, <i>anteiso</i>-C_{17 : 0}, <i>iso</i>-C_16:0 and <i>iso</i>-C_15:0. The polar lipids detected included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannosides. Based on 16S rRNA gene sequence analysis, strains NRAIS3^T and NRAIS4 showed the highest similarity (99.4%) to the type strains <i>Streptomyces fodineus</i> TW1S1^T, <i>Streptomyces puniciscabiei</i> DSM 41929^T and <i>Streptomyces filipinensis</i> JCM 4369^T. The average nucleotide identity based on MUMmer and digital DNA-DNA hybridization values between the genomes of the two strains and those of related type strains were significantly below the <i>Streptomyces</i> species delineation thresholds of 96.7% and 70%, respectively. The ethyl acetate crude extract of NRAIS3^T exhibited antibacterial activity against Gram-positive and Gram-negative pathogenic bacteria. It showed the highest activity against <i>Listeria monocytogenes</i> ATCC 7644, followed by <i>Staphylococcus epidermidis</i> ATCC 12228, and <i>Enterococcus faecium</i> ATCC 35667. Liquid chromatography-mass spectrometry and gas chromatography-mass spectrometry analyses revealed diverse antimicrobial metabolites, including aminoquinolines, ergopeptines, isoflavones, hydroxycinnamic acids, <i>N</i>-alkyl piperazines, benzotriazoles, benzimidazoles, phenylacetamides, as well as volatile compounds such as 2,5,5-trimethylcyclohexane-1,3-dione, hexamethyl-cyclotrisiloxane and 1,4-bis(trimethylsilyl) benzene. Based on the taxonomic results, strains NRAIS3^T and NRAIS4 represent a novel species within the genus <i>Streptomyces</i>, for which the name <i>Streptomyces mitragynae</i> sp. nov. is proposed. The type strain is NRAIS3^T (=LMG 34056^T=TBRC 20459^T).