RESEARCH ARTICLE Metabolomic profiling and biological investigation of the marine sponge‐derived bacterium Rhodococcus sp. UA13 Yasmin Elsayed 1 | John Refaat 1 | Usama Ramadan Abdelmohsen 1,2 | Eman Maher Othman 3,4 | Helga Stopper 4 | Mostafa Ahmed Fouad 1 1 Department of Pharmacognosy, Faculty of Pharmacy, Minia University, Minia, Egypt 2 Department of Botany II, Julius‐von‐Sachs Institute for Biological Sciences, University of Würzburg, Würzburg, Germany 3 Department of Analytical Chemistry, Faculty of Pharmacy, Minia University, Minia, Egypt 4 Department of Toxicology, University of Würzburg, Würzburg, Germany Correspondence John Refaat, Pharmacognosy Department, Faculty of Pharmacy, Minia University, 61519 Minia, Egypt. Email: johnrefaat82@yahoo.com Abstract Introduction: Marine sponge‐associated actinomycetes are potent sources of bio- active 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 liq- uid 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 IC 50 values of 9.3, 6.7, and 8.7 μg/mL, respectively, whereas only the ethyl acetate fraction was active against Chlamydia trachomatis (IC 50 = 18.9 μg/mL). In contrast, both fractions did not exert anti‐infective actions against Enterococcus faecalis and Leishmania major, whereas the methanol frac- tion 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 spec- trometry (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 actinomycetes, anti‐infective, biological activities, LC–MS, marine sponges, metabolomics, Rhodococcus Received: 4 January 2018 Revised: 17 February 2018 Accepted: 17 February 2018 DOI: 10.1002/pca.2765 Phytochemical Analysis. 2018;1–6. Copyright © 2018 John Wiley & Sons, Ltd. wileyonlinelibrary.com/journal/pca 1