Taxonomic and Metabolomics Profiling of Actinobacteria Strains from Himalayan Collection Sites in Pakistan

Abstract

Actinobacteria have proven themselves as the major producers of bioactive compounds with wide applications. In this study, 35 actinobacteria strains were isolated from soil samples collected from the Himalayan mountains region in Pakistan. The isolated strains were identified by polyphasic taxonomy and were prioritized based on biological and chemical screening to identify the strains with ability to produce inimitable metabolites. The biological screening included antimicrobial activity against Staphylococcus aureus, Micrococcus luteus, Salmonella enterica, Escherichia coli, Mycobacterium aurum, and Bacillus subtilis and anticancer activity using human cancer cell lines PC3 and A549. For chemical screening, methanolic extracts were investigated using TLC, HPLC-UV/MS. The actinobacteria strain PU-MM93 was selected for scale-up fermentation based on its unique chemical profile and cytotoxicity (50-60% growth inhibition) against PC3 and A549 cell lines. The scale-up fermentation of PU-MM93, followed by purification and structure elucidation of compounds revealed this strain as a promising producer of the cytotoxic anthracycline aranciamycin and aglycone SM-173-B along with the potent neuroprotective carboxamide oxachelin C. Other interesting metabolites produced include taurocholic acid as first report herein from microbial origin, pactamycate and cyclo(L-Pro-L-Leu). The study suggested exploring more bioactive microorganisms from the untapped Himalayan region in Pakistan, which can produce commercially significant compounds.

Fig. 1

Work-up scheme of the metabolites produced by Streptomyces sp. PU-MM93

Fig. 2

Cytotoxicity of actinobacteria extracts against A549 (non-small cell lung cancer) and PC3 (prostate cancer) human cell lines

Fig. 3

A Anti Gram-positive activities of generated extracts produced by the Himalayan isolated actinobacteria strains. B Anti Gram-negative and antifungal activities of generated extracts produced by the Himalayan isolated actinobacteria strains

Fig. 4

Chemical structures of compounds 1–6, produced by Streptomyces sp. PU-MM93

Fig. 5

A % Viability of A549 (non-small cell lung cancer) and PC3 (prostate) human cancer cell lines (after 72 h) at 5.0 μM concentration of compounds 1–6. B Dose–response of compound 1 against A549 (non-small cell lung cancer) human cancer cell line (72 h). C Dose–response of compound 1 against PC3 (prostate) human cancer cell line (72 h). A549: IC₅₀ for the compounds 1 (2.78 μM), 2 (> 10 μM) and 3–6 (> 20 μM). PC3: IC₅₀ for the compounds 1 (0.68 μM), 2 (> 10 μM) and 3–6 (> 20 μM)

Fig. 6

Antimicrobial activity of compounds 1–6 produced by Streptomyces sp. PU-MM93 (% growth of the test strains at 200 μM concentration determined by spectrophotometric method at OD 600 nm)

Fig. 7

Axolotl screening assay of compounds (1–6) isolated from Streptomyces sp. PU-MM93 (after 7 days, at 10 μM concentration). Vehicle (DMSO) was used as the negative control and the Hsp90 inhibitor geldanamycin was used as a positive control