Effects of different media and solvents on biological activities and secondary metabolites profiles of a coral-derived Streptomyces sp. RC4
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Abstract. Rizky, Nofiani R, Rudiyansyah, Putri CD, Setiawan A, Wibowo DS, Setiyoningrum F. 2025. Effects of different media and solvents on biological activities and secondary metabolites profiles of a coral-derived Streptomyces sp. RC4. Biodiversitas 26: 739-747. Streptomyces sp. RC4 demonstrates a potential source of secondary metabolites with various biological activities. Culture media and solvents for culture media influence the production of the metabolites. This study investigated the effect of different culture media and solvents on the biological activities and secondary metabolite profiles of Streptomyces sp. RC4. Seven different media, i.e., International Streptomyces Project (ISP) 1, ISP2, ISP4, A1, Starch Casein Broth (SCB), Potato Dextrose Broth (PDB), and PC-1, were used as growth media. Three different solvents, i.e., distilled water, 2.5% NaCl solution, and artificial seawater (ASW), were used to prepare each medium. The cultures were then shaken at 200 rpm for seven days, after which secondary metabolites were extracted with ethyl acetate. Each extract was tested for antibacterial activity and cytotoxicity using brine shrimp lethality assays (BSLT). The result showed that 11 of 21 extracts exhibited antimicrobial activity with varying levels of effectiveness. ISP2 extract (ISP2 dissolved in distilled water) demonstrated the largest inhibition zones, while SCB NaCl extract (SCB dissolved in 2.5% NaCl solution) inhibited the highest number of test microbes. Three extracts (ISP2, PC-1 ASW, and SCB NaCl extracts) were classified as highly toxic based on Clarkson’s toxicity category (LC50 < 100 µg/mL). The most toxic extract was PC-1 ASW extract (PC-1 dissolved in ASW) with an LC50 value of 40 ?g/mL. Metabolomic analysis revealed distinct chemical profiles for each extract, with secondary metabolites such as cyclo (Leu-Pro), cyclo (Pro-Val), p-cymene, o-cymene, and methoxy-phenyl oxime. Several compounds remained unidentified through molecular networking analysis, suggesting they might be novel. These findings indicated the diversity of secondary metabolites and biological activities of Streptomyces sp. RC4 is significantly influenced by medium and solvent compositions.
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References
Aksenov AA, Laponogov I, Zhang Z et al. 2021. Auto-deconvolution and molecular networking of gas chromatography-mass spectrometry data. Nat Biotechnol 39 (2): 169-173. DOI: 10.1038/s41587-020-0700-3.
Balahbib A, El Omari N, Hachlafi NEL, Lakhdar F, El Menyiy N, Salhi N, Mrabti HN, Bakrim S, Zengin G, Bouyahya A. 2021. Health beneficial and pharmacological properties of p-cymene. Food Chem Toxicol 153: 112259-112275. DOI: 10.1016/j.fct.2021.112259.
Belknap KC, Park CJ, Barth BM, Andam CP. 2020. Genome mining of biosynthetic and chemotherapeutic gene clusters in Streptomyces bacteria. Sci Rep 10 (1): 2003. DOI: 10.1038/s41598-020-58904-9.
Chambers MC, MacLean B, Burke R et al. 2012. A cross-platform toolkit for mass spectrometry and proteomics. Nat Biotechnol 30 (10): 918-920. DOI: 10.1038/nbt.2377.
Chen X, He Y, Ye H, Xie Y, Sen B, Jiao N, Wang G. 2020. Different carbon and nitrogen sources regulated docosahexaenoic acid (DHA) production of Thraustochytriidae sp. PKU#SW8 through a fully functional polyunsaturated fatty acid (PUFA) synthase gene (pfaB). Bioresour Technol 318: 124273-124280. DOI: 10.1016/j.biortech.2020.124273.
Chipps E, Jayini R, Ando S, Protzman A, Muhi M, Mottaleb M, Malkawi A, Islam M. 2012. Cytotoxicity analysis of active components in bitter melon (Momordica charantia) seed extracts using human embryonic kidney and colon tumor cells. Nat Prod 7 (9): 1203-1208. DOI: 10.4489/MYCO.2009.37.3.211.
Cimmino A, Bejarano A, Masi M, Puopolo G, Evidente A. 2021. Isolation of 2,5-diketopiperazines from Lysobacter capsici AZ78 with activity against Rhodococcus fascians. Nat Prod Res 35 (23): 4969-4977. DOI: 10.1080/14786419.2020.1756803.
Das V, Chatterjee NS, Pushpakaran PU, Lalitha KV, Joseph TC. 2023. Exploration of natural product repository by combined genomics and metabolomics profiling of mangrove-derived Streptomyces murinus THV12 strain. Fermentation 9 (6): 576-593. DOI: 10.3390/fermentation9060576.
Fu J, Xie X, Zhang S, Kang N, Zong G, Zhang P, Cao G. 2023. Rich organic nitrogen impacts clavulanic acid biosynthesis through the arginine metabolic pathway in Streptomyces clavuligerus F613-1. Microbiol Spectr 11 (1): e02017-22. DOI: 10.1128/spectrum.02017-22.
Jeli? D, Antolovi? R. 2016. From erythromycin to azithromycin and new potential ribosome-binding antimicrobials. Antibiotics 5 (3): 29-42. DOI: 10.3390/antibiotics5030029.
Kim J, Kim JC, Sang MK. 2023. Identification of isomeric cyclo(leu-pro) produced by Pseudomonas sesami BC42 and its differential antifungal activities against Colletotrichum orbiculare. Front MIcrobiol 14: 1230345. DOI: 10.3389/fmicb.2023.1230345.
Li Y, Gong N, Zhou L, Yang Z, Zhang H, Gu Y, Ma J, Ju J. 2024. OSMAC-based discovery and biosynthetic gene clusters analysis of secondary metabolites from marine-derived Streptomyces globisporus SCSIO LCY30. Mar Drug 22 (1): 21-35. DOI: 10.3390/md22010021.
Liu J, Clarke JA, McCann S, Hillier NK, Tahlan K. 2022. Analysis of Streptomyces volatilomes using global molecular networking reveals the presence of metabolites with diverse biological activities. Microbiol Spectr 10 (4): e00552-22. DOI: 10.1128/spectrum.00552-22.
Liu Z, Zhao Y, Huang C, Luo Y. 2021. Recent advances in silent gene cluster activation in Streptomyces. Front Bioeng Biotechnol 9: 632230. DOI: 10.3389/fbioe.2021.632230.
Locatelli FM, Goo KS, Ulanova D. 2016. Effects of trace metal ions on secondary metabolism and the morphological development of Streptomycetes. Metallomics 8: 469-480. DOI: 10.1039/c5mt00324e.
Martens H, Karstang T, Næs T. 1987. Improved selectivity in spectroscopy by multivariate calibration. J Chemomet 1: 201-219. DOI: 10.1002/cem.1180010403.
Martín-Aragón VR, Millán FR, Cuadrado C, Daranas AH, Medarde AF, López JMS. 2023. Induction of new aromatic polyketides from the marine actinobacterium Streptomyces griseorubiginosus through an OSMAC Approach. Mar Drug 21: 526-540. DOI: 10.3390/md21100526.
Meena DK, Sahoo AK, Swain HS, Borah S, Srivastava PP, Sahu NP, Das BK. 2020. Prospects and perspectives of virtual in-vitro toxicity studies on herbal extracts of Terminalia arjuna with enhanced stratagem in Artemia salina model: A panacea to explicit the credence of solvent system in brine shrimp lethality bioassay. Emirates J Food Agric 32 (1): 25-37. DOI: 10.9755/EJFA.2020.V32.I1.2055.
Meyer BN, Ferrigni NR, Putnam JE, Jacobsen LB, Nichols DE, Mclaughlin JL. 1982. Brine shrimp: A convenient general bioassay for active plant constituents. J Med Plant Res 45: 31-34. DOI: 10.1055/s-2007-971236.
Nofiani R, Ardiningsih P, Rudiyansyah, Padupu D, Rizky, Amalia DA, Octaviana S, Sukito A, Setiyoningrum F, Weisberg AJ, Mahmud T. 2024. Biological activities and metabolomic profiles of extracts from the marine sediment bacterium Nocardiopsis alba DP1B cultivated in different media. Microb Pathogen 192: 106702-106713. DOI: 10.1016/j.micpath.2024.106702.
Nofiani R, Rudiyansyah, Ardiningsih P, Rizky, Zahra STA, Sukito A, Weisberg AJ, Chang JH, Mahmud T. 2023. Genome features and secondary metabolite potential of the marine symbiont Streptomyces sp. RS2. Archives Microbiol 205 (6): 244-255. DOI: 10.1007/s00203-023-03556-2.
Nofiani R, Weisberg AJ, Tsunoda T, Panjaitan RGPP, Brilliantoro R, Chang JH, Philmus B, Mahmud T. 2020. Antibacterial potential of secondary metabolites from Indonesian marine bacterial symbionts. Intl J Microbiol 2020 (1): 8898631. DOI: 10.1155/2020/8898631.
Omeke JN, Anaga AO, Okoye JA. 2018. Brine shrimp lethality and acute toxicity tests of different hydro-methanol extracts of Anacardium occidentale using in vitro and in vivo models: A preliminary study. Comparative Clin Pathol 27 (6): 1717-1721. DOI: 10.1007/s00580-018-2798-y.
Onaka H, Mori Y, Igarashi Y, Furumai T. 2011. Mycolic acid-containing bacteria induce natural-product biosynthesis in Streptomyces species. Appl Environ Microbiol 77: 400-406. DOI: 10.1128/AEM.01337-10.
Pan R, Bai X, Chen J, Zhang H, Wang H, Aon JC. 2019. Exploring structural diversity of microbe secondary metabolites using OSMAC strategy: A literature review. Front Microbiol 10: 294. DOI: 10.3389/fmicb.2019.00294.
Pardo-Esté C, Cortés J, Castro-Severyn J, Pérez V, Henriquez-Aedo K, Cuadros F, Yañez C, Cuadros-Orellana S, Dorador C, Molina V, Eissler Y, Paquis P, Jeffrey WH, Pozo P, Pérez PA, Hengst MB. 2024. Secondary metabolites with antimicrobial activity produced by thermophilic bacteria from a high-altitude hydrothermal system. Front Microbiol 15: 1477458. DOI: 10.3389/fmicb.2024.1477458.
Quinn GA, Banat AM, Abdelhameed AM, Banat IM. 2020. Streptomyces from traditional medicine: Sources of new innovations in antibiotic discovery. J Med Microbiol 69: 1040-1048. DOI: 10.1099/jmm.0.001232.
Rammali S, Rahim A, El Aalaoui M, Bencharki B, Dari K, Habach A, Abdeslam L, khattabi A. 2024. Antimicrobial potential of Streptomyces coeruleofuscus SCJ isolated from microbiologically unexplored garden soil in Northwest Morocco. Sci Rep 14 (1): 3359. DOI: 10.1038/s41598-024-53801-x.
Ripa FA, Nikkon F, Zaman S, Khondkar P. 2009. Optimal conditions for antimicrobial metabolites production from a new Streptomyces sp. RUPA-08PR isolated from Bangladeshi soil. Mycobiology 37 (3): 211-214. DOI: 10.4489/MYCO.2009.37.3.211.
Salman M, Tariq A, Mustafa G, Javed MR, Naheed S, Qamar SA. 2022. Cyclo(L-Leucyl-L-Prolyl) from Lactobacillus coryniformis BCH-4 inhibits the proliferation of Aspergillus flavus: An in vitro to in silico approach. Arch Microbiol 204 (5): 267. DOI: 10.1007/s00203-022-02884-z.
Schmid R, Heuckeroth S, Korf et al. 2023. Integrative analysis of multimodal mass spectrometry data in MZmine 3. Nat Biotechnol 41 (4): 447-449. DOI: 10.1038/s41587-023-01690-2.
Shannon P, Markiel A, Ozier O, Nitin SB, Wang TJ, Ramage D, Amin N, Schwikowski B, Ideker T. 2003. Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genom Res 13 (11): 2498-2504. DOI: 10.1101/gr.1239303.metabolite.
Shirling EB, Gottlieb D. 1966. Methods for characterization of Streptomyces species. Intl J Syst Bacteriol 16 (3): 313-340. DOI: 10.1099/00207713-16-3-313.
Subramani R, Aalbersberg W. 2012. Marine actinomycetes: An ongoing source of novel bioactive metabolites. Microbiol Res 167 (10): 571-580. DOI: 10.1016/j.micres.2012.06.005.
Tanamatayarat P. 2016. Antityrosinase, antioxidative activities, and brine shrimp lethality of ethanolic extracts from Protium serratum (Wall. ex Colebr.) Engl. Asian Pac J Trop Biomed 6 (12): 1050-1055. DOI: 10.1016/j.apjtb.2016.10.001.
Tangerina MMP, Furtado LC, Leite VMB, Bauermeister A, Velasco-Alzate K, Jimenez PC, Garrido LM, Padilla G, Lopes NP, Costa-Lotufo LV, Pena Ferreira MJ. 2021. Metabolomic study of marine Streptomyces sp.: Secondary metabolites and the production of potential anticancer compounds. PLoS One 15 (12): e0244385. DOI: 10.1371/journal.pone.0244385.
Tawaha KA. 2006. Cytotoxicity evaluation of Jordanian wild plants using brine shrimp lethality test. Jordan J Appl Sci-Nat Sci 8 (1): 12-17.
Tian F, Woo SY, Lee SY, Chun HS. 2018. p-Cymene and its derivatives exhibit antiaflatoxigenic activities against Aspergillus flavus through multiple modes of action. Appl Biol Chem 61 (5): 489-497. DOI: 10.1007/s13765-018-0382-4.
Ullah MO, Haque M, Urmi KF, Abu AH, Anita E., Begum M, Hamid K. 2013. Anti-bacterial activity and brine shrimp lethality bioassay of methanolic extracts of fourteen different edible vegetables from Bangladesh. Asian Pac J Trop Biomed 3: 1-7. DOI: 10.1016/S2221-1691(13)60015-5.
Wang M, Carver JJ, Phelan VV et al. 2016. Sharing and community curation of mass spectrometry data with global natural products social molecular networking. Nat Biotechnol 34 (8): 828-837. DOI: 10.1038/nbt.3597.
Zhang Y, Feng, L, Hemu, X, Tan, NH, Wang Z. 2024. OSMAC strategy: A promising way to explore microbial cyclic peptides. Eur J Med Chem 268: 116175-116207. DOI: 10.1016/j.ejmech.2024.116175.
Zong G, Fu J, Zhang P, Zhang W, Xu Y, Cao G, Zhang R. 2022. Use of elicitors to enhance or activate the antibiotic production in Streptomyces. Crit Rev Biotechnol 42: 1260-1283. DOI: 10.1080/07388551.2021.1987856.
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