Nontargeted Metabolomics of Streptomyces Sourced from Thailand Reveals the Presence of Bioactive Metabolites

Abstract

Actinobacteria are widely recognized as prolific producers of bioactive metabolites with diverse biological properties, yet they remain largely unexplored. In this study, we investigated the antimicrobial potential and chemical diversity of crude extracts from actinobacterial strains isolated from mangrove sediments collected in Chonburi and Chachoengsao provinces of Thailand. Taxonomic identification confirmed that these isolates belong to the genus Streptomyces. Notably, ten isolates, identified as Streptomyces iranensis, Streptomyces yogyakartensis, Streptomyces cacaoi, Streptomyces ardesiacus, Streptomyces phaeoluteichromatogenes, and Streptomyces albiaxialis, exhibited potent inhibitory activity against chloroquine-resistant Plasmodium falciparum K1 at concentrations <10 μg/mL. Among these, only S. albiaxialis displayed anti-human immunodeficiency virus-1 viral protein R (HIV-1 Vpr) activity in HeLa cells harboring the TREx plasmid encoding full-length Vpr (TREx-HeLa-Vpr cells). MS/MS-guided molecular networking analysis highlighted the metabolic complexity of the isolates, revealing a diverse array of distinct compounds. These included chymostatin B, geldanamycin, dehydroxynocardamine, ikarugamycin epoxide, kanchanamycin C, glochidone, bisucaberin, coproporphyrin III, futalosine, and various siderophores such as ferrioxamine B, desferrioxamine D2, desferrioxamine G, desferrioxamine E, desferrioxamine, desferrioxamine H, and ferrioxamine E. Moreover, guided by the potent antimalarial activity of strain S2-SC19, the compound elaiophylin was detected, isolated, and identified using analytical techniques. Remarkably, the compound exhibited potent antimalarial activity with an IC₅₀ value of 0.002 ± 0.002 μg/mL against P. falciparum K1. Furthermore, genomic analysis revealed that strain S2-SC19 is most closely related to Streptomyces asiaticus DSM no. 41761. This study highlights Thai mangrove soil as a valuable source of bioactive compounds, including elaiophylin, and underscores the bioactive potential and chemical diversity of mangrove ecosystems as a rich, untapped reservoir of natural products.

Figure 1

Collection sites of environmental samples for actinobacteria isolation in Thailand.

Figure 2

Anti-Vpr activities (green) of the selected Thai actinobacterial isolates and methanolic extracts and their cytotoxicities (red). Data are expressed as mean ± SD (n = 3) and analyzed using one-way ANOVA followed by Tukey’s post hoc test. The same letters (a, b, and c) when compared to the positive control damnacanthal (2.5, 5, 10 μg/mL) group indicate significance at p < 0.05. And the * and ** indicate significance p < 0.05 when compared between groups except among each other. Statistical significance for the samples that showed average to good vpr inhibitory activity was only presented.

Figure 3

Neighbor joining phylogenetic tree based on almost complete 16S rRNA gene sequences of potent Thai actinobacterial isolates from mangrove sediments demonstrates the relationships with their closely related type strains. Numbers at the nodes indicate levels of bootstrap support based on an analysis of 1,000 resampled data sets. The scale bar indicates 0.01 substitution per nucleotide position.

Figure 4

Bioactive actinobacterial molecular network (MN) and clusters of putative bioactive metabolites annotated in positive ion mode by using mass spectrometry. Node colors: red = S2-SC19; blue = 1–3; violet = S4-SC11; orange = S5-SC2; green = S7-SC9.

Figure 5

Bioactive actinobacterial molecular network (MN) and clusters of putative bioactive metabolites annotated in negative ion mode by using mass spectrometry. Node colors: red = S2-SC19; blue = 1–3; violet = S4-SC11; orange = S5-SC2; green = S7-SC9.

Figure 6

Alignment of the elaiophylin BGC from the MIBiG database with the predicted elaiophylin-like BGCs found in regions 27.2, 50.2, 66.1, and 133.1 of Actinobacteria strain S2-SC19. Genes are color-coded based on their functional groups, and homologous genes are connected by shaded regions that indicate the percentage of amino acid identity between their protein products.

Figure 7

Alignment of the geldanamycin BGC from the MIBiG database with the predicted geldanamycin-like BGCs found in region 1.3 of Actinobacteria strain S2-SC19. Genes are color-coded based on their functional groups, and homologous genes are connected by shaded regions that indicate the percentage of amino acid identity between their protein products.