Characterization and biological activity of new natural products from Streptomyces alboniger BA2

Natural products are secondary metabolites produced by plants, fungi, and microorganisms, possessing various bioactivities. Among these, microbial metabolites exhibit a range of chemical structures and are utilized as drugs in the fight against diseases due to their antimicrobial, anticancer, antiviral, and antidiabetic activities. Actinomycetes are a significant source of natural microbial metabolites, with Streptomyces species being among the most important sources of bioactive products. Antibiotics produced by these bacteria, such as streptomycin, cephalosporin, chloramphenicol, and tetracycline, have ushered in the antibiotic era in medicine. The overuse of antibiotics has led to the rapid spread of resistance among bacteria, resulting in the emergence of new antibiotic-resistant hospital pathogens. Therefore, there is an urgent need for the discovery of new antimicrobial compounds with various mechanisms of action. Different strategies are available for the discovery of new antibiotics with diverse chemical structures. These include isolating new bacteria from unusual environments, cultivating them using innovative culture strategies, and rapidly and accurately identifying the metabolites they produce using omics approaches. In recent years, a significant number and variety of new bioactive metabolites have been discovered using genomic and metabolomic approaches. Our research group previously isolated, characterized, and sequenced the genome of Streptomyces alboniger BA2 from plant roots. It was found that there are a high number of biosynthetic gene clusters (BGCs) responsible for the synthesis of secondary metabolites in the genome; however, most of these gene clusters were not active in the culture medium. In light of this information, the aim of this study is to reveal the potential for producing new natural products by activating the biosynthetic gene clusters of S. alboniger through different culture strategies. To achieve this, S. alboniger was cultivated in solid and liquid culture regimes in the presence of two different plant hormones, indole-3-acetic acid (IAA) and jasmonic acid (JA). The metabolites were extracted using organic solvents, and the antibacterial activities of the extracts were determined. The metabolites were analyzed using LC-MS/MS metabolomic approaches. S. alboniger BA2 was grown in M2 liquid medium in the presence of different concentrations of IAA and JA until reaching the stationary phase. The cultures were extracted with ethyl acetate, and antimicrobial activity was investigated using the disk diffusion method. Six different test organisms were used for antimicrobial activity screening. S. alboniger BA2 was also cultivated in solid media containing IAA and JA and was analyzed in vivo against the aforementioned test organisms using the cross-streak method. The compounds and metabolite profiles contained in the extracts were identified by analyzing the LC-MS/MS data against compound libraries in the GNPS database. It was observed that S. alboniger BA2, produced in liquid culture medium, has a broad spectrum and high potency antimicrobial activity against both Gram-negative and Gram-positive test organisms. Although no increase in antimicrobial effect was observed in the presence of plant hormones compared to the control, the results of metabolomic studies revealed the presence of compounds not previously detected in this isolate by S. alboniger BA2 in both liquid and solid media. In the presence of only IAA, microbial metabolites such as futalosine, 3-hydroxyoctanoic acid, and quinoxaline-2-carboxylic acid were dereplicated, while in the presence of only JA, futalozin was dereplicated. In antimicrobial metabolite analyses from solid culture, Streptomyces sp. BA2 isolate and test organisms were co-cultured in the presence of JA. According to these results, the taxifolin compound isolated from the zone against E. coli and the newly identified compound B27A19, which is listed in the GNPS database but whose structure has not yet been elucidated, also dereplicated against E. coli and K. pneumoniae. This study is significant not only for uncovering previously unreported antimicrobial activities and new metabolites from the S. alboniger BA2 isolate, but also for demonstrating that innovative culture strategies and different culture regimes result in variations in microbial metabolite production profiles.