Molecular Networking Analysis and Antibacterial Potential of Ethyl Acetate Extracts of Sinomicrobium sp. PAP.21 using OSMAC Method
![](/public/site/images/admin/icons/icon-doi.png)
Harwoko Harwoko(1*), Anggun Tri Rahmawati(2), Riyanti Riyanti(3)
(1) Department of Pharmacy, Faculty of Health Sciences, Universitas Jenderal Soedirman, Purwokerto, Central Java
(2) Department of Pharmacy, Faculty of Health Sciences, Universitas Jenderal Soedirman, Purwokerto, Central Java
(3) Faculty of Fisheries and Marine Science, Universitas Jenderal Soedirman, Purwokerto, Central Java
(*) Corresponding Author
Abstract
Challenges in drug discovery include biosynthetic gene clusters which remain silent under standard laboratory culture conditions. On the other hand, the rediscovery of the known compounds is inevitable. Accordingly, One Strain-MAny Compounds (OSMAC) approach and molecular networking analysis are currently applicable to discovering new bioactive compounds. Sinomicrobium sp. PAP.21 isolated from marine sediment collected in Cenderawasih Bay, West Papua, was added to the culture. Then, the bacterium was cultured in five different liquid media (RL1, A1BFe+C, NB, LB, and seawater) and incubated for 4, 5, and 7 days. The bacterial cultures were extracted using ethyl acetate (EtOAc) separately for each medium and incubation period, followed by LC-HRMS measurement. A total of 45 ethyl acetate extracts were assayed for in vitro antibacterial activity against Micrococcus luteus and Escherichia coli. Molecular networking analysis through GNPS indicated that three putative compounds possess antibacterial properties. EtOAc extracts from the A1BFe+C medium demonstrated antibacterial activity against M. luteus. However, none of them were active against E. coli. Collectively, Sinomicrobium sp. PAP.21 produced bioactive compounds exhibiting antibacterial potential, particularly against Gram-positive bacteria.
Keywords
References
Agarwal, H., Bajpai, S., Mishra, A., Kohli, I., Varma, A., Fouillaud, M., Dufossé, L., & Joshi, N. C. (2023). Bacterial Pigments and Their Multifaceted Roles in Contemporary Biotechnology and Pharmacological Applications. Microorganisms, 11(3), 1–19. https://doi.org/10.3390/microorganisms11030614.
Ambarwati, A., Wahyuono, S., Moeljopawiro, S., & Yuwono, T. (2020). Antimicrobial activity of ethyl acetate extracts of Streptomyces sp. CRB46 and the prediction of their bioactive compounds chemical structure. Biodiversitas, 21(7), 3380–3390. https://doi.org/10.13057/biodiv/d210763
Antimicrobial Resistance Collaborators. (2022). Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. The Lancet, 399(10325), 629–655. https://doi.org/10.1016/S0140-6736(21)02724-0.
Balouiri, M., Sadiki, M., & Ibnsouda, S. K. (2016). Methods for in vitro evaluating antimicrobial activity: A review. Journal of Pharmaceutical Analysis, 6(2), 71–79. https://doi.org/10.1016/j.jpha.2015.11.005.
Becam, J., Walter, T., Burgert, A., Schlegel, J., Sauer, M., Seibel, J., & Schubert-Unkmeir, A. (2017). Antibacterial activity of ceramide and ceramide analogs against pathogenic Neisseria. Scientific Reports, 7(1), 1–12. https://doi.org/10.1038/s41598-017-18071-w.
Bonnet, M., Lagier, J. C., Raoult, D., & Khelaifia, S. (2019). Bacterial culture through selective and non-selective conditions: the evolution of culture media in clinical microbiology. New Microbes and New Infections, 34. https://doi.org/10.1016/j.nmni.2019.100622.
Brinkmann, S., Kurz, M., Patras, M. A., Hartwig, C., Marner, M., Leis, B., Billion, A., Kleiner, Y., Bauer, A., Toti, L., Pöverlein, C., Hammann, P. E., Vilcinskas, A., Glaeser, J., Spohn, M., & Schäberle, T. F. (2021). Genomic and Chemical Decryption of the Bacteroidetes Phylum for Its Potential to Biosynthesize Natural Products. Microbiology Spectrum, 10(3), 1–27. https://doi.org/10.1128/spectrum.02479-21.
Cheng, B., Li, C., Lai, Q., Du, M., Shao, Z., Xu, P., & Yang, C. (2014). Sinomicrobium pectinilyticum sp. nov., A pectinase-producing bacterium isolated from alkaline and saline soil, and emended description of the genus Sinomicrobium. International Journal of Systematic and Evolutionary Microbiology, 64, 2939–2943. https://doi.org/10.1099/ijs.0.061671-0.
Choi, E. J., Nam, S. J., Paul, L., Beatty, D., Kauffman, C. A., Jensen, P. R., & Fenical, W. (2015). Previously Uncultured Marine Bacteria Linked to Novel Alkaloid Production. Chemistry and Biology, 22(9), 1270–1279. https://doi.org/10.1016/j.chembiol.2015.07.014.
Davis, W. W., & Stout, T. R. (1971). Disc plate method of microbiological antibiotic assay. II. Novel procedure offering improved accuracy. Applied Microbiology, 22(4), 666–670. https://doi.org/10.1128/aem.22.4.666-670.1971.
Esposito, F. P., Giugliano, R., Sala, G. Della, Vitale, G. A., Buonocore, C., Ausuri, J., Galasso, C., Coppola, D., Franci, G., Galdiero, M., & de Pascale, D. (2021). Combining OSMAC approach and untargeted metabolomics for the identification of new glycolipids with potent antiviral activity produced by a marine Rhodococcus. International Journal of Molecular Sciences, 22(16). https://doi.org/10.3390/ijms22169055.
Gavriilidou, A., Gutleben, J., Versluis, D., Forgiarini, F., Van Passel, M. W. J., Ingham, C. J., Smidt, H., & Sipkema, D. (2020). Comparative genomic analysis of Flavobacteriaceae: Insights into carbohydrate metabolism, gliding motility and secondary metabolite biosynthesis. BMC Genomics, 21(1), 1–21. https://doi.org/10.1186/s12864-020-06971-7.
Hamill, P. G., Stevenson, A., McMullan, P. E., Williams, J. P., Lewis, A. D. R., Sudharsan, S., Stevenson, K. E., Farnsworth, K. D., Khroustalyova, G., Takemoto, J. Y., Quinn, J. P., Rapoport, A., & Hallsworth, J. E. (2020). Microbial lag phase can be indicative of, or independent from, cellular stress. Scientific Reports, 10(1), 1–20. https://doi.org/10.1038/s41598-020-62552-4.
Jegatheesan, A., Sudhakar, M. P., Poonam, C., Perumal, K., & Arunkumar, K. (2017). Isolation and characterization of alginate-degrading bacteria Sinomicrobium oceani. Biomass Conversion and Biorefinery, 7(1), 51–58. https://doi.org/10.1007/s13399-016-0212-z.
Judith, T., Fourie, & Chianella. (2022). Antimicrobial properties of English churchyard lichens. Access Microbiology, 1–25.
Khan, M. S., Gao, J., Munir, I., Zhang, M., Liu, Y., Moe, T. S., Xue, J., & Zhang, X. (2021). Characterization of Endophytic Fungi, Acremonium sp., from Lilium davidii and Analysis of Its Antifungal and Plant Growth-Promoting Effects. BioMed Research International, 2021. https://doi.org/10.1155/2021/9930210.
Li, L.F., Xu, L., Li, W.-H., & Sun, J.-Q. (2022). Sinomicrobium kalidii sp. nov., an indole-3-acetic acid-producing endophyte from a shoot of halophyte Kalidium cuspidatum. International Journal of Systematic and Evolutionary Microbiology, 72(7). https://doi.org/https://doi.org/10.1099/ijsem.0.005452.
Li, M., Wang, K., Jia, C., Liu, T., Yang, S., Ou, H., & Zhao, J. (2021). Bacteroidetes bacteria, important players in the marine sponge larval development process. IScience, 24(6), 102662. https://doi.org/10.1016/j.isci.2021.102662.
Liu, X., Lai, Q., Du, Y., Zhang, X., Zhong, H., & Shao, Z. (2019). Sinomicrobium soli sp. nov., isolated from arctic soil. International Journal of Systematic and Evolutionary Microbiology, 69(4), 1070–1074. https://doi.org/10.1099/ijsem.0.003273.
López-Rodríguez, M., López-Rosales, L., Necci, G. D., Cerón-García, M. del C., Navarro-López, E., Gallardo-Rodríguez, J. J., Tristán, A. I., Abreu, A. C., & García-Camacho, F. (2022). The Isolation of Specialty Compounds from Amphidinium carterae Biomass by Two-Step Solid-Phase and Liquid-Liquid Extraction. Toxins, 14, 1–19.
Manalu, R. T. (2017). Isolation and characterization of degrading hydrocarbons bacteria from Indonesia. Sainstech Farma, 10(2), 23–28.
Matin, M. M., Bhuiyan, M. M. ., Debnath, D. C., & Manchur, M. A. (2013). Synthesis and comparative antimicrobial studies of some acylated d-glucofuranose and d-glucopyranose derivatives. International Journal of Biosciences (IJB), 3(8), 279–287. https://doi.org/10.12692/ijb/3.8.279-287.
Mohimani, H., Gurevich, A., Shlemov, A., Mikheenko, A., Korobeynikov, A., Cao, L., Shcherbin, E., Nothias, L. F., Dorrestein, P. C., & Pevzner, P. A. (2018). Dereplication of microbial metabolites through database search of mass spectra. Nature Communications, 9(1), 1–12. https://doi.org/10.1038/s41467-018-06082-8.
Nasab, M. O., & Khodakaramian, G. (2022). The Inhibitory Activity of Some Endophytic Bacteria from Satureja Khuzestanica Leaves against Phythopathogenic Bacteria. Biological Journal of Microorganism, 11(44), 145–158.
Pinedo-Rivilla, C., Aleu, J., & Durán-Patrón, R. (2022). Cryptic Metabolites from Marine-Derived Microorganisms Using OSMAC and Epigenetic Approaches. Marine Drugs, 20(2), 1–34. https://doi.org/10.3390/md20020084.
Prihanto, A. A., Timur, H. D. L., Jaziri, A. A., Nurdiani, R., & Pradarameswari, K. A. (2018). Isolation and Identification endophytic bacteria mangrove Sonneratia alba gelatinase enzyme producer from the beach Sendang Biru, Malang, East Java. Indonesia Journal of Halal, 1(1), 31–42. https://doi.org/10.14710/halal.v1i1.3114.
Pringgenies, D., Wilis, A. ., Feliatra, F., & Ariyanto, D. (2023). The antibacterial and antifungal potential of marine natural ingredients from the symbiont bacteria of mangrove. Global Journal of Environmental Science and Management, 9(4), 1–14. https://doi.org/10.22035/gjesm.2023.04.
Purves, K., Macintyre, L., Brennan, D., Hreggviðsson, G., Kuttner, E., Ásgeirsdóttir, M. E., Young, L. C., Green, D. H., Edrada-Ebel, R., & Duncan, K. R. (2016). Using molecular networking for microbial secondary metabolite bioprospecting. Metabolites, 6(1). https://doi.org/10.3390/metabo6010002.
Ranković, B. (2019). Lichen secondary metabolites: Bioactive properties and pharmaceutical potential. In Springer. https://doi.org/10.1007/978-3-319-13374-4.
Riyanti, Balansa, W., Liu, Y., Sharma, A., Mihajlovic, S., Hartwig, C., Leis, B., Rieuwpassa, F. J., Ijong, F. G., Wägele, H., König, G. M., & Schäberle, T. F. (2020a). Selection of sponge-associated bacteria with high potential for the production of antibacterial compounds. Scientific Reports, 10(1), 1–14. https://doi.org/10.1038/s41598-020-76256-2.
Riyanti, Marner, M., Hartwig, C., Patras, M. A., Wodi, S. I. M., Rieuwpassa, F. J., Ijong, F. G., Balansa, W., & Schäberle, T. F. (2020b). Sustainable Low-Volume Analysis of Environmental Samples by Semi-Automated Prioritization of Extracts for Natural Product Research ( SeaPEPR ). Marine Drugs, 18(649), 1–15.
Riyanti, Zumkeller, C. M., Spohn, M., Mihajlovic, S., Schwengers, O., Goesmann, A., Riviani, R., Meinita, M. D. N., Schäberle, T. F., & Harwoko, H. (2023). Draft Genome Sequence of Sinomicrobium sp . Strain PAP.21, Isolated from a Coast Sample of Papua, Indonesia. Microbiology Resource Announcements, 20–22.
Schneider, Y. K., Jørgensen, S. M., Andersen, J. H., & Hansen, E. H. (2021). Qualitative and quantitative comparison of liquid–liquid phase extraction using ethyl acetate and liquid–solid phase extraction using poly-benzyl-resin for natural products. Applied Sciences, 11(21). https://doi.org/10.3390/app112110241.
Spyere, A., Rowley, D. C., Jensen, P. R., & Fenical, W. (2003). New neoverrucosane diterpenoids produced by the marine gliding bacterium Saprospira grandis. Journal of Natural Products, 66(6), 818–822. https://doi.org/10.1021/np0205351.
Tangerina, M. M. P., Furtado, L. C., Leite, V. M. B., Bauermeister, A., Velasco-Alzate, K., Jimenez, P. C., Garrido, L. M., Padilla, G., Lopes, N. P., Costa-Lotufo, L. V., & Pena Ferreira, M. J. (2020). Metabolomic study of marine Streptomyces sp.: Secondary metabolites and the production of potential anticancer compounds. PLoS ONE, 15(12), 1–19. https://doi.org/10.1371/journal.pone.0244385.
Thawabteh, A. M., Swaileh, Z., Ammar, M., Jaghama, W., Yousef, M., Karaman, R., A. Bufo, S., & Scrano, L. (2023). Antifungal and Antibacterial Activities of Isolated Marine Compounds. Toxins, 15(2), 1–21. https://doi.org/10.3390/toxins15020093.
Tortorella, E., Tedesco, P., Esposito, F. P., January, G. G., Fani, R., Jaspars, M., & De Pascale, D. (2018). Antibiotics from deep-sea microorganisms: Current discoveries and perspectives. Marine Drugs, 16(10), 1–16. https://doi.org/10.3390/md16100355.
Wang, M., Carver, J., Phelan, V. et al. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nat Biotechnol 34, 828–837 (2016). https://doi.org/10.1038/nbt.3597
Wang, F., Li, M., Huang, L., & Zhang, X. H. (2021). Cultivation of uncultured marine microorganisms. Marine Life Science and Technology, 3(2), 117–120. https://doi.org/10.1007/s42995-021-00093-z.
Wibowo, J. T., Kellermann, M. Y., Versluis, D., Putra, M. Y., Murniasih, T., Mohr, K. I., Wink, J., Engelmann, M., Praditya, D. F., Steinmann, E., & Schupp, P. J. (2019). Biotechnological potential of bacteria isolated from the sea cucumber Holothuria leucospilota and Stichopus vastus from Lampung, Indonesia. Marine Drugs, 17(11). https://doi.org/10.3390/md17110635.
Wu, P., Ren, H., Zhu, Q., Mei, Y., Liang, Y., & Chen, Z. (2022). Sinomicrobium weinanense sp. nov., a halophilic bacterium isolated from saline-alkali soil. International Journal of Systematic and Evolutionary Microbiology, 72(4). https://doi.org/https://doi.org/10.1099/ijsem.0.005282.
Xu, Y., Tian, X. P., Liu, Y. J., Li, J., Kim, C. J., Yin, H., Li, W. J., & Zhang, S. (2013). Sinomicrobium oceani gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from marine sediment. International Journal of Systematic and Evolutionary Microbiology, 63, 1045–1050. https://doi.org/10.1099/ijs.0.041889-0.
![](/public/site/images/admin/icons/icon-doi.png)
Article Metrics
![](/public/site/images/admin/icons/icon-graph.png)
Refbacks
- There are currently no refbacks.
Copyright (c) 2024 Majalah Obat Tradisional
![Creative Commons License](http://i.creativecommons.org/l/by-nc-nd/4.0/88x31.png)
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.
Faculty of Pharmacy
Universitas Gadjah Mada