Bioprospecting secondary metabolites with antimicrobial properties from soil bacteria in high-temperature ecosystems

Abstract Background The ongoing emergence and spread of drug-resistant pathogens necessitate urgent solutions. Natural products from bacterial sources are recognized as a promising source of antibiotics. This study aimed to isolate and characterize soil microorganisms from extremely hot environments and to screen their secondary metabolites for antibacterial activity. Methods Bacterial isolates were identified using standard culture techniques. Primary and secondary screenings for antimicrobial activity were conducted using the Modified Kirby-Bauer antibiotic susceptibility test against five bacterial species. Based on the efficacy of antimicrobial activity against these target pathogens, the isolate Pseudomonas sp. strain ASTU00105 was selected for further characterization through whole genomic sequencing. Secondary metabolites were analyzed using GC–MS, and antioxidant activities were also evaluated. Results A total of 76 isolates were identified, and their secondary metabolites were tested against Escherichia coli, Salmonella typhi, Acinetobacter baumannii, Staphylococcus aureus, Streptococcus pyogenes, and Candida albicans. Seventeen isolates (22.37%) exhibited antimicrobial activity. Isolate ASTU00105 exhibited the highest activity against all the test organisms and was selected for further analysis. Whole-genome sequencing using the Nanopore MinION sequencer revealed that strain ASTU00105 belonged to the genus Pseudomonas with the highest similarity (95.97%) to Pseudomonas stutzeri, and designated as Pseudomonas sp. strain ASTU00105. Upon Average Nucleotide Identity (ANI) analysis, the strain exhibited 87.81% sequence similarity with genes of the closest type strain, suggesting its novelty and distinctiveness within the Pseudomonas genus. The genomic analysis of the isolated strain revealed 6 biosynthetic gene cluster (BGC) genes dispersed throughout the entire genome, which are implicated in the synthesis of antimicrobial secondary metabolites. The major chemical compounds detected in the EtAc extracts as detected by gas chromatography-mass spectrometry (GC–MS) were phenol, 2,5-bis (1,1-dimethylethyl) (36.6%), followed by 1,2-Benzenedicarboxylic acid, diethyl ester (12.22%), Eicosane (9.71%), Dibutyl phthalate (3.93%), and 1-Dodecanol (2.34%). In conclusion Pseudomonas sp. strain ASTU00105 exhibited the greatest potential for producing secondary metabolites with significant antimicrobial activity.