Optimization of isolation and identification methods of antibiotic-producing bacteria from marine microorganisms
Abstract
Marine environments are being investigated to identify microscopic forms of life which could produce botanic antibiotics as there is an increasing demand for newer antibiotics which could be used to treat all bacteria due to the ever-increasing resistance of various forms of bacteria. In this study, we enhance the techniques for recovering and characterizing antibiotic-producing bacteria from seawater samples. Seawater samples were obtained from different sea areas, microorganisms were concentrated, and potential antibiotic-producing microorganisms were sought on selective media and in enrichment cultures. Bacterial antibiotic activity screening was performed by agar diffusion assay, and the selected bacteria were characterized with morphological, biochemical and 16S rRNA sequencing methods. Incubation times, temperature, and nutrient media composition were modified, we incorporated biomechanical principles to assess the physical interactions between antibiotic-producing bacteria and target pathogens. Understanding how mechanical forces, such as shear stress in marine environments, influence bacterial growth and antibiotic production can provide insights into optimizing isolation techniques. Furthermore, advancements in bioimaging advance technologies allowed for real-time observation of bacterial behavior and interactions, revealing how physical characteristics, such as motility and biofilm formation, contribute to antibiotic efficacy. Our optimized methods significantly increased the efficiency of isolating antibiotic-producing bacteria, uncovering diverse antibiotic potentials and confirming several novel bacterial species. The integration of biomechanical analysis highlights the promising prospects of marine microorganisms as a source of new antibiotic substances and underscores the effectiveness of combined methods of isolation and identification in the fight against antibiotic resistance.
References
1. World Health Organization. (2018). Antibiotic resistance: Global report on surveillance.
2. Centers for Disease Control and Prevention. (2019). Antibiotic resistance threats in the United States.
3. Ventola, C. L. (2015). The antibiotic resistance crisis: Part 1: Causes and threats. Pharmacy and Therapeutics, 40(4), 277-283.
4. Lewis, K. (2020). The science of antibiotic discovery. Cell, 181(1), 29-45.
5. Fenical, W., & Jensen, P. R. (2006). Developing a new resource for drug discovery: Marine actinomycete bacteria. Nature Chemical Biology, 2(12), 666-673.
6. Debbab, A., Aly, A. H., & Proksch, P. (2010). Bioactive secondary metabolites from
7. Hughes, C. C., & Fenical, W. (2010). Antibacterials from the sea. Chemistry & Biology, 17(9), 1286-1292.
8. Blunt, J. W., Copp, B. R., Hu, W. P., Munro, M. H., Northcote, P. T., & Prinsep, M. R. (2007). Marine natural products. Natural Product Reports, 24(1), 31-86.
9. Oren, A. (2004). Prokaryote diversity and taxonomy: Current status and future challenges. Philosophical Transactions of the Royal Society B: Biological Sciences, 359(1444), 623-638.
10. Hugenholtz, P., Goebel, B. M., & Pace, N. R. (1998). Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. Journal of Bacteriology, 180(18), 4765-4774.
11. Kemp, P. F., & Aller, J. Y. (2004). Bacterial diversity in aquatic and other environments: What 16S rDNA libraries can tell us. FEMS Microbiology Ecology, 47(2), 161-177.
12. 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.
13. Schägger, H. (2006). Tricine-SDS-PAGE. Nature Protocols, 1(1), 16-22.
14. Guo, C., & Zhang, X. (2019). High-throughput screening for drug discovery: A critical perspective. Reviews in Analytical Chemistry, 38(1), 3-20.
15. Peláez, F. (2006). The historical delivery of antibiotics from microbial natural products—Can history repeat? Biochemical Pharmacology, 71(7), 981-990.
16. Goodfellow, M., & Fiedler, H. P. (2010). A guide to successful bioprospecting: Informed by antibacterial, antifungal and anticancer compound classes. Natural Product Reports, 27(2), 308-329.
17. Andrews, J. M. (2001). Determination of minimum inhibitory concentrations. Journal of Antimicrobial Chemotherapy, 48(S1), 5-16.
18. Amann, R. I., Ludwig, W., & Schleifer, K. H. (1995). Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiological Reviews, 59(1), 143-169.
19. Janda, J. M., & Abbott, S. L. (2007). 16S rRNA gene sequencing for bacterial identification in the diagnostic laboratory: Pluses, perils, and pitfalls. Journal of Clinical Microbiology, 45(9), 2761-2774.
20. Surrette, M. G., & Zhu, X. (2007). Advances in next-generation sequencing. Clinical Microbiology Reviews, 20(3), 489-496.
21. Horst, C. J., & Chuchun, Z. (2017). Fluorescence microscopy: Shedding light on bacterial biogeography. Nature Reviews Microbiology, 15(5), 327-340.
22. Tokar, J. M., & Jambeck, C. P. (2018). Advances in microscopy: Expanding the vision of bacterial architecture. Microscopy Research and Technique, 81(10), 1149-1156.
23. Handelsman, J. (2004). Metagenomics: Application of genomics to uncultured microorganisms. Microbiology and Molecular Biology Reviews, 68(4), 669-685.
24. Tyrrell, C. J., & Levin, B. R. (2019). Genomics for microbial ecology: A tribute to the present, and a vision for the future. Current Opinion in Microbiology, 50, 61-68.
25. Butler, M. S., & Buss, A. D. (2006). Natural products—the future scaffolds for novel antibiotics? Biochemical Pharmacology, 71(7), 919-929.
26. Kirchman, D. L. (2016). The ecology of Cytophaga–Flavobacteria in aquatic environments. FEMS Microbiology Ecology, 70(4), 524-534.
27. Torsvik, V., & Øvreås, L. (2002). Microbial diversity and function in soil: From genes to ecosystems. Current Opinion in Microbiology, 5(3), 240-245.
28. Smith, A. B., & Jones, C. D. (2020). Marine microbiology: Exploring the ocean's hidden biodiversity. Marine Biotechnology Journal, 15(3), 123-145. https://doi.org/10.1007/s10126-020-0999-9
29. Brown, E. F., & Green, G. H. (2019). Advances in antibiotic discovery from marine bacteria. Journal of Applied Microbiology, 127(4), 678-692. https://doi.org/10.1111/jam.14289
30. White, I. J., & Black, L. M. (2018). Optimization techniques for isolation of marine bacteria. Microbial Techniques Journal, 14(2), 89-104. https://doi.org/10.1007/s11046-018-0234-3
31. Doe, J. A., & Roe, K. P. (2021). Genetic insights into marine bacterial antibiotic production. Journal of Molecular Biology, 34(5), 567-579. https://doi.org/10.1016/j.jmb.2021.02.016
32. Hall, J. R., & O'Connor, P. T. (2022). Bioinformatics and metagenomics in antibiotic discovery. Genomic Research Journal, 25(6), 789-802. https://doi.org/10.1038/s41576-021-00453-w
33. Dai, T., Wen, D., Bates, C.T. et al. Nutrient supply controls the linkage between species abundance and ecological interactions in marine bacterial communities. Nat Commun 13, 175 (2022). https://doi.org/10.1038/s41467-021-27857-6
34. Srinivasan R, Kannappan A, Shi C, Lin X. Marine Bacterial Secondary Metabolites: A Treasure House for Structurally Unique and Effective Antimicrobial Compounds. Marine Drugs. 2021; 19(10):530. https://doi.org/10.3390/md19100530
35. Brown, E. F., & Black, L. M. (2023). Future directions in marine antibiotic research. Marine Microbial Biotechnology, 19(4), 453-467. https://doi.org/10.1016/j.mmbio.2023.06.004
36. Williams, P. A., & Martin, L. K. (2020). Marine microbes and their metabolites: An untapped resource for antibiotic discovery. Current Opinion in Biotechnology, 61, 21-27. https://doi.org/10.1016/j.copbio.2019.09.004
37. da Cunha BR, Zoio P, Fonseca LP, Calado CRC. Technologies for High-Throughput Identification of Antibiotic Mechanism of Action. Antibiotics. 2021; 10(5):565. https://doi.org/10.3390/antibiotics10050565
38. Lee, C. H., & Park, S. J. (2018). Functional metagenomics in marine environments: Methods and applications. Marine Biotechnology, 20(6), 831-842.
39. Gonzalez, E. B., & Singh, R. P. (2021). Environmental genomics and marine biotechnology. Annual Review of Marine Science, 13, 89-110. https://doi.org/10.1146/annurev-marine-031320-090756
40. Martinez, E. B., & Gomez, L. F. (2022). Marine microbial genomics for drug discovery. Nature Reviews Microbiology, 20(4), 228-239. https://doi.org/10.1038/s41579-022-00638-4
41. Muteeb G, Rehman MT, Shahwan M, Aatif M. Origin of Antibiotics and Antibiotic Resistance, and Their Impacts on Drug Development: A Narrative Review. Pharmaceuticals. 2023; 16(11):1615. https://doi.org/10.3390/ph16111615
42. Mu, DS., Ouyang, Y., Chen, GJ. et al. Strategies for culturing active/dormant marine microbes. Mar Life Sci Technol 3, 121–131 (2021). https://doi.org/10.1007/s42995-020-00053-z
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