Metabolomic profiling and biological investigation of the marine sponge-derived bacterium Rhodococcus sp. UA13

Abstract

Introduction: Marine sponge-associated actinomycetes are potent sources of bioactive natural products of pharmaceutical significance. They also contributed to the discovery of several clinically relevant antimicrobials.

Objective: To apply the non-targeted metabolomics approach in chemical profiling of the sponge-derived bacterium Rhodococcus sp. UA13, formerly recovered from the Red Sea sponge Callyspongia aff. Implexa, along with testing for the anti-infective potential of its different fractions.

Methodology: Metabolomic analysis of the crude extract was carried out using liquid chromatography with high resolution electrospray ionisation mass spectrometry (LC-HR-ESI-MS) for dereplication purposes. Besides, the three major fractions (ethyl acetate, methanol, and n-butanol) obtained by chromatographic fractionation of the crude extract were evaluated for their anti-infective properties.

Results: A variety of metabolites, mostly peptides, were characterised herein for the first time from the genus Rhodococcus. Among the tested samples, the n-butanol fraction showed potent inhibitory activities against Staphylococcus aureus, Candida albicans, and Trypanosoma brucei brucei with IC₅₀ values of 9.3, 6.7, and 8.7 μg/mL, respectively, whereas only the ethyl acetate fraction was active against Chlamydia trachomatis (IC₅₀ = 18.9 μg/mL). In contrast, both fractions did not exert anti-infective actions against Enterococcus faecalis and Leishmania major, whereas the methanol fraction was totally inactive against all the tested organisms.

Conclusion: This study showed the helpfulness of the established procedure in metabolic profiling of marine actinomycetes using liquid chromatography mass spectrometry (LC-MS) data, which aids in reducing the complex isolation steps during their chemical characterisation. The anti-infective spectrum of their metabolites is also interestingly relevant to future drug development.

Keywords: LC-MS; Rhodococcus; actinomycetes; anti-infective; biological activities; marine sponges; metabolomics.