Metabolite profiling of endophytic Streptomyces spp. and its antiplasmodial potential

Abstract

Background: Antiplasmodial drug discovery is significant especially from natural sources such as plant bacteria. This research aimed to determine antiplasmodial metabolites of Streptomyces spp. against Plasmodium falciparum 3D7 by using a metabolomics approach.

Methods: Streptomyces strains' growth curves, namely SUK 12 and SUK 48, were measured and P. falciparum 3D7 IC₅₀ values were calculated. Metabolomics analysis was conducted on both strains' mid-exponential and stationary phase extracts.

Results: The most successful antiplasmodial activity of SUK 12 and SUK 48 extracts shown to be at the stationary phase with IC₅₀ values of 0.8168 ng/mL and 0.1963 ng/mL, respectively. In contrast, the IC₅₀ value of chloroquine diphosphate (CQ) for antiplasmodial activity was 0.2812 ng/mL. The univariate analysis revealed that 854 metabolites and 14, 44 and three metabolites showed significant differences in terms of strain, fermentation phase, and their interactions. Orthogonal partial least square-discriminant analysis and S-loading plot putatively identified pavettine, aurantioclavine, and 4-butyldiphenylmethane as significant outliers from the stationary phase of SUK 48. For potential isolation, metabolomics approach may be used as a preliminary approach to rapidly track and identify the presence of antimalarial metabolites before any isolation and purification can be done.

Keywords: Anti-plasmodial; Metabolomics; Multivariate analysis; Plasmodium falciparum; Streptomyces.

Figure 1. Growth curve of Streptomyces spp.

(A) The growth curve of Streptomyces sp. SUK 12 and (B) SUK 48.

Figure 2. Two-way analysis of variance (ANOVA).

The red circle with 155 metabolites represents type of strain, SUK 12 and SUK 48, whereas blue circle with 125 metabolites represents fermentation time and green circle with 103 metabolites represents interaction between both (time and strain type).

Figure 3. Principal component analysis.

(A) PCA scores scatter plot of SUK 12 (day 5 and 12) and SUK 48 (day 7 and 14) crude extracts (R2 = 0.47; and Q2 = 0.271). (B) OPLS-DA scores scatter plot between SUK 12 and SUK 48 crude extracts (R2(Y) = 0.651; Q2 = 0.395). (C) OPLS-DA scores scatter plot between S48D7 and S48D14, (R2(Y) = 0.996; Q2 = 0.61). (D) S-plot of SUK 48 day 7 vs. day 14 metabolites.

Figure 4. Total ion chromatogram.

Total ion chromatogram of the crude extract of SUK48 on day 14 with labelled of significant peaks of outliers (1–6).

Figure 5. Phylogenetic tree.

Phylogenetic tree of full length 16S rRNA nucleotide sequences using Neighbour Joining method showing the relationship of strain SUK12 and SUK 48 with closely related members of the genus Streptomyces and Kitasatospora setae KM-6054^T as the outgroup. Numbers at the nodes indicate levels of bootstrap support based on 1,000 replication. Bar, 0.005 changes per nucleotide.