Antibacterial diketopiperazines from marine sponge-associated Actinobacteria against multidrug-resistant bacteria
Article Sidebar
Abstract Views: 729
File Views: 397
Main Article Content
Abstract
Abstract. Larasati A, Budiarti S, Lestari Y. 2025. Antibacterial diketopiperazines from marine sponge-associated Actinobacteria against multidrug-resistant bacteria. Biodiversitas 26: 6480-6489. The global rise of Multidrug-Resistant (MDR) bacterial infections has created an urgent demand for new antibacterial agents. Marine actinomycetes, particularly those associated with marine sponges, are considered a promising source of bioactive secondary metabolites. This study explored the antibacterial potential of 12 actinobacterial isolates obtained from the marine sponge Callyspongia sp., collected from the waters of Kepulauan Seribu, Indonesia. Among these, the isolate Cal24h exhibited the highest antibacterial activity. Based on previous 16S rRNA gene sequence analysis, this isolate was identified as Streptomyces tendae. Optimization of its culture conditions significantly enhanced inhibition zones against four MDR bacterial strains: 18.57±0.08 mm for Enteropathogenic Escherichia coli (EPEC) K1.1, 19.70±0.09 mm for Pseudomonas aeruginosa, 20.09±0.20 mm for Bacillus subtilis, and 20.54±0.31 mm for Methicillin-Resistant Staphylococcus aureus (MRSA). The Minimum Inhibitory Concentration (MIC) values of the ethyl acetate extract ranged from 62.5 to 125 µg/mL. Further analysis using GC-MS and LC-MS revealed the presence of diketopiperazine compounds, including Cyclo(Leu-Pro), Cyclo(L-Pro-L-Val), and Cyclo(Pro-Phe), all known for their antibacterial properties. Notably, this study is the first to report the use of a modified A1 medium to enhance antibacterial metabolite production in sponge-derived Streptomyces, representing a novel cultivation strategy. Cultivation in A1 medium yielded the highest extract quantity and exhibited the strongest antibacterial activity among all media tested. This study provides the first diketopiperazine production by S. tendae associated with the Indonesian sponge Callyspongia sp., thereby underscoring the untapped potential of sponge-derived actinobacteria as promising sources of antibacterial compounds against multidrug-resistant pathogens.
Article Details
Issue
Section
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.
References
Ahaddin AY, Budiarti S, Mustopa AZ, Darusman HS, Triratna L. 2021. Short Communication: Acute toxicity study of plantaricin from Lactobacillus plantarum S34 and its antibacterial activity. Biodiversitas 22 (1): 227-232. DOI: 10.13057/biodiv/d220128.
Ahmed I, Asgher M, Sher F, Hussain SM, Nazish N, Joshi N, Sharma A, Parra-Saldívar R, Bilal M, Iqbal HMN. 2022. Exploring marine as a rich source of bioactive peptides: Challenges and opportunities from marine pharmacology. Mar Drugs 20: 208. DOI: 10.3390/md20030208.
Al-Bari MAA, Bhuiyan MSA, Flores ME, Petrosyan P, García-Varela M, Ul Islam MA. 2005. Streptomyces bangladeshensis sp. nov., isolated from soil, which produces bis-(2-ethylhexyl)phthalate. Intl J Syst Evol Microbiol 55: 1973-1977. DOI: 10.1099/ijs.0.63516-0.
Alshaibani M, Mohamad Zin N, Jalil J, Sidik N, Ahmad SJ, Kamal N, Edrada-Ebel R. 2017. Isolation, purification, and characterization of five active diketopiperazine derivatives from endophytic Streptomyces SUK 25 with antimicrobial and cytotoxic activities. J Microbiol Biotechnol 27 (7): 1249-1256. DOI: 10.4014/jmb.1608.08032.
Aziz SS, Al Saiqali M, Begum N, Najmuddin M. 2025. GC-MS characterization and therapeutic potential of phytochemical constituents of the Unani Medicine Uterotibb’s aqueous alkaline extract. Haya Saudi J Life Sci 10 : 146-156. DOI: 10.36348/sjls.2025.v10i05.001.
Bahrami Y, Bouk S, Kakaei E, Taheri M. 2022. Natural products from Actinobacteria as a potential source of new therapies against colorectal cancer: A review. Front Pharmacol 13: 929161. DOI: 10.3389/fphar.2022.929161.
Bhakyashree K, Kannabiran K. 2020. Actinomycetes mediated targeting of drug resistant MRSA pathogens. J King Saud Univ Sci 32 (1): 260-264. DOI: 10.1016/j.jksus.2018.04.034.
Borthwick AD. 2012. 2,5-Diketopiperazines: synthesis, reactions, medicinal chemistry, and bioactive natural products. Chemical Reviews 112 (7): 3641-3716. DOI: 10.1021/cr200398y.
Cao DD, Van Trinh TT, Mai HDT, Vu VN, Le HM, Thi QV, Nguyen MA, Duong TT, Tran DT, Chau VM, Ma R, Shetye G, Cho S, Murphy BT, Pham VC. 2019. Antimicrobial lavandulylated flavonoids from a sponge-derived Streptomyces sp. G248 in East Vietnam Sea. Mar Drugs 17 (9): 529. DOI: 10.3390/md17090529.
Castaldi S, Cimmino A, Masi M, Evidente A. 2022. Bacterial lipodepsipeptides and some of their derivatives and cyclic dipeptides as potential agents for biocontrol of pathogenic bacteria and fungi of agrarian plants. J Agric Food Chem 70 (15): 4591-4598. DOI: 10.1021/acs.jafc.1c08139.
Challis GL, Hopwood DA. 2003. Synergy and contingency as driving forces for the evolution of multiple secondary metabolite production by Streptomyces species. Proc Nat Acad Sci USA 100: 14555-14561. DOI: 10.1073/pnas.1934677100.
Chatterjee S, Karmakar A, Azmi SA, Barik A. 2018. Antibacterial activity of long-chain primary alcohols from Solena amplexicaulis leaves. Proc Zool Soc 71: 313-319. DOI: 10.1007/s12595-017-0208-0.
Cheng Y, Chen N, Li J, Su J-C, Yang J, Zhang C-X, Lin H-W, Zhou Y. 2021. Antimicrobial chlorinated carbazole alkaloids from the sponge‐associated actinomycete Streptomyces diacarni LHW51701. Chin J Chem 39 (5): 1188-1192. DOI: 10.1002/cjoc.202000736.
Chu M-J, Li M, Ma H, Li P-L, Li G-Q. 2022. Secondary metabolites from marine sponges of the genus Agelas: A comprehensive update insight on structural diversity and bioactivity. RSC Adv 12 (13): 7789-7820. DOI: 10.1039/d1ra08765g.
Čihák M, Kameník Z, Šmídová K, Bergman N, Benada O, Kofroňová O, Petříčková K, Bobek J. 2017. Secondary metabolites produced during the germination of Streptomyces coelicolor. Front Microbiol 8: 2495. DOI: 10.3389/fmicb.2017.02495.
CLSI. 2023. Performance Standards for Antimicrobial Susceptibility Testing. Clinical and Labortory Standards Institute, Pennsylvania.
de Athayde AE, de Araujo CES, Sandjo LP, Biavatti MW. 2024. UPLC-ESI-QToF-MS metabolomics comparison between wild and cultivated Porophyllum ruderale, a non-conventional edible plant. Rev Bras Farmacogn 34: 750-757. DOI: 10.1007/s43450-024-00521-y.
Djebbah FZ, Belyagoubi L, Abdelouahid DE, Kherbouche F, Al-Dhabi NA, Arasu MV, Ravindran B. 2021. Isolation and characterization of novel Streptomyces strain from Algeria and its in-vitro antimicrobial properties against microbial pathogens. J Infect Public Health 14 (11): 1671-1678. DOI: 10.1016/j.jiph.2021.09.019.
EUCAST. 2024. Breakpoint tables for interpretation of MICs and zone diameters,. European Committee on Antimicrobial Susceptibility Testing, Sweden. http://www.eucast.org/clinical_breakpoints/.
Gunes H, Gulen D, Mutlu R, Gumus A, Tas T, Topkaya AE. 2016. Antibacterial effects of curcumin: An in vitro minimum inhibitory concentration study. Toxicol Ind Health 32 (2): 246-250. DOI: 10.1177/0748233713498458.
Hanif N, Murni A, Tanaka C, Tanaka J. 2019. Marine natural products from Indonesian waters. Mar Drugs 17: 364. DOI: 10.3390/md17060364.
Hong L-L, Ding Y-F, Zhang W, Lin H-W. 2022. Chemical and biological diversity of new natural products from marine sponges: A review (2009-2018). Mar Life Sci Technol 4: 356-372. DOI: 10.1007/s42995-022-00132-3.
Hossain TJ. 2024. Methods for screening and evaluation of antimicrobial activity: A review of protocols, advantages, and limitations. Eur J Microbiol Immunol 14 (2): 97-115. DOI: 10.1556/1886.2024.00035.
Huang X, Kong F, Zhou S, Huang D, Zheng J, Zhu W. 2019. Streptomyces tirandamycinicus sp. nov., a novel marine sponge-derived actinobacterium with antibacterial potential against Streptococcus agalactiae. Front Microbiol 10: 482. DOI: 10.3389/fmicb.2019.00482.
Jamal Q, Cho J-Y, Moon J-H, Kim KY. 2017. Purification and antifungal characterization of cyclo(d-Pro-l-Val) from Bacillus amyloliquefaciens Y1 against Fusarium graminearum to control head blight in wheat. Biocatal Agric Biotechnol 10: 141-147. DOI: 10.1016/j.bcab.2017.01.003.
Kumar NS, Nath VS, Chandran RP, Nambisan B. 2014. Cyclic dipeptides from rhabditid entomopathogenic nematode-associated Bacillus cereus have antimicrobial activities. World J Microbiol Biotechnol 30 (2): 439-449. DOI: 10.1007/s11274-013-1461-7.
Larasati A, Ryandini D, Oedjijono, Kusharyati DF. 2021. Optimization of medium and incubation time in the production of antibacterial compounds by Streptomyces sp. SA404. In: 10th International Seminar and 12th Congress of Indonesian Society for Microbiology (ISISM 2019). Advances in Biological Sciences Research; Atlantis Press, Dordrecht, Netherlands. DOI: 10.2991/absr.k.210810.008.
Li P, Lu H, Zhang Y, Zhang X, Liu L, Wang M, Liu L. 2023. The natural products discovered in marine sponge-associated microorganisms: Structures, activities, and mining strategy. Front Mar Sci 10: 1191858. DOI: 10.3389/fmars.2023.1191858.
Li W, Ding L, Li J, Wen H, Liu Y, Tan S, Yan X, Shi Y, Lin W, Lin H-W, He S. 2022. Novel antimycin analogues with agricultural antifungal activities from the sponge-associated Actinomycete Streptomyces sp. NBU3104. J Agric Food Chem 70 (27): 8309-8316. DOI: 10.1021/acs.jafc.2c02626.
Liang J, She J, Fu J, Wang J, Ye Y, Yang B, Liu Y, Zhou X, Tao H. 2023. Advances in natural products from the marine-sponge-associated microorganisms with antimicrobial activity in the last decade. Mar Drugs 21 (4): 236. DOI: 10.3390/md21040236.
Malisorn K, Embaen S, Sribun A, Saeng-in P, Phongsopitanun W, Tanasupawat S. 2020. Short Communication: Identification and antimicrobial activities of Streptomyces, Micromonospora, and Kitasatospora strains from rhizosphere soils. J Appl Pharm Sci 10 (2):123-128. DOI: 10.7324/japs.2020.102018.
Mary TRJ, Kannan RR, Iniyan AM, Ranjith WAC, Nandhagopal S, Vishwakarma V, Vincent SGP. 2021. β-lactamase inhibitory potential of kalafungin from marine Streptomyces in Staphylococcus aureus infected zebrafish. Microbiol Res 2020: 126666. DOI: 10.1016/j.micres.2020.126666.
Mehbub MF, Yang Q, Cheng Y, Franco CMM, Zhang W. 2024. Marine sponge-derived natural products: Trends and opportunities for the decade of 2011-2020. Front Mar Sci 11: 1462825. DOI: 10.3389/fmars.2024.1462825.
Ortlieb N, Klenk E, Kulik A, Niedermeyer THJ. 2021. Development of an agar-plug cultivation system for bioactivity assays of actinomycete strain collections. PLoS One 16 (11): e0258934. DOI: 10.1371/journal.pone.0258934.
Pahira DSJ, Damayanti E, Lisdiyanti P, Mustofa, Hertiani T. 2023. Exploring the potency of Streptomyces koyangensis strain SHP 9-3 isolated from the soil of Enggano Island (Indonesia) as an antibacterial source. Biodiversitas 24 (3): 1460-1466. DOI: 10.13057/biodiv/d240315.
Rahman A, Siddiqui SA, Rahman MO, Kang SC. 2019. Cyclo(L-Pro-L-Tyr) from Streptomyces sp. 150: Exploiting in vitro potential in controlling foodborne pathogens and phytopathogens. Anti-Infect Agents 18: 169-177. DOI: 10.2174/2211352517666190716155147.
Retnowati D, Solihin DD, Ghulamahdi M, Lestari Y. 2019. Characterization of sponge-associated actinobacteria with potential to promote plant growth on tidal swamps. J Biol Res Boll Soc Ital Biol Sper 92 (2): 8191. DOI: 10.4081/jbr.2019.8191.
Retnowati W, Mertaniasih NM, Purwanta M, Wiqoyah N, Atika, Maharani S, Mahdani W. 2023. Antibiotic-producing Streptomyces sp. isolated from the soil of a mangrove ecosystem. Folia Medica Indonesiana 59 (3): 238-245. DOI: 10.20473/fmi.v59i3.45806.
Risan MH, Subhi SA, Hussain BY. 2022. Evaluating the inhibitory effect of Streptomyces bacteria against pathogenic bacteria and study its compatibility with some antibiotic types. Biomed Chem Sci 1 (2): 35-40. DOI: 10.48112/bcs.v1i2.75.
Romano G, Almeida M, Coelho AV, Cutignano A, Gonçalves LG, Hansen E, Khnykin D, Mass T, Ramšak A, Rocha MS, Silva TH, Sugni M, Ballarin L, Genevière A-M. 2022. Biomaterials and bioactive natural products from marine invertebrates: From basic research to innovative applications. Mar Drugs 20 (4): 219. DOI: 10.3390/md20040219.
Ryandini D, Pramono H, Sukanto S. 2018. Antibacterial activity of Streptomyces SAE4034 isolated from Segara Anakan mangrove Rhizosphere against antibiotic resistant bacteria. Biosaintifika J Biol Biol Educ 10 (1): 117-124. DOI: 10.15294/biosaintifika.v10i1.12896.
Saadouli I, El Euch IZ, Trabelsi E, Mosbah A, Redissi A, Ferjani R, Fhoula I, Cherif A, Sabatier J-M, Sewald N, Ouzari H-I. 2020. Isolation, characterization and chemical synthesis of large spectrum antimicrobial cyclic dipeptide (L-leu-l-pro) from Streptomyces misionensis v16r3y1 bacteria extracts. a novel1H NMR metabolomic approach. Antibiotics 9 (5): 270. DOI: 10.3390/antibiotics9050270.
Santos ACC, Malta SM, Dantas RCC, Rocha NDC, de Carvalho Azevedo VA, Ueira-Vieira C. 2022. Antimicrobial activity of supernatants produced by bacteria isolated from Brazilian stingless bee’s larval food. BMC Microbiol 22 (1): 127. DOI: 10.1186/s12866-022-02548-4.
Sari DCAF, Ningsih F, Yabe S, Yokota A, Oetari A, Sjamsuridzal W. 2021. Antibacterial activity of a thermophilic actinobacterium Streptomyces cellulosae SL2-2-R-9 on different growth media. J Phys: Conf Ser 1943: 012099. DOI: 10.1088/1742-6596/1943/1/012099.
Setiawati S, Nuryastuti T, Sholikhah EN, Lisdiyanti P, Pratiwi SUT, Sulistiyani TR, Ratnakomala S, Jumina, Mustofa. 2021. The potency of Actinomycetes extracts isolated from Pramuka Island, Jakarta, Indonesia as antimicrobial agents. Biodiversitas 22 (3): 1104-1111. DOI: 10.13057/biodiv/d220304.
Seukep AJ, Tamambang FM, Matieta VY, Mbuntcha HG, Bomba FDT, Kuete V, Ndip LMA. 2025. Potential of methanol extracts of Nephelium lappaceum (Sapindaceae) and Hyphaene thebaica (Arecaceae) as adjuvants to enhance the efficacy of antibiotics against critical class priority bacteria. PLoS One 20 (2): e0314958. DOI: 10.1371/journal.pone.0314958.
Siro G, Donald L, Pipite A. 2023. The diversity of deep-sea Actinobacteria and their natural products: An epitome of curiosity and drug discovery. Diversity 15 (1): 30. DOI: 10.3390/d15010030.
Somasundaram S, Arulmani SRB, Ganesan G. 2024. Screening and characterization of antagonistic Streptomyces sp. JS20 from marine sediment in Vaan Island. Microbe 4: 100106. DOI: 10.1016/j.microb.2024.100106.
Sugiyama Y, Oya A, Kudo T, Hirota A. 2010. Surugapyrone a from Streptomyces coelicoflavus strain usf-6280 as a new dpph radical-scavenger. J Antibiot 63 (7): 365-369. DOI: 10.1038/ja.2010.60.
Tang KWK, Millar BC, Moore JE. 2023. Antimicrobial Resistance (AMR). Br J Biomed Sci 80: 11387. DOI: 10.3389/bjbs.2023.11387.
Tao S, Wang Y, Hong R, Huang S-H. 2022. Potent antibiotic Lemonomycin: A glimpse of its discovery, origin, and chemical synthesis. Molecules 27: 4324. DOI: 10.3390/molecules27134324.
Tornberg-Belanger SN, Rwigi D, Mugo M et al. 2022. Antimicrobial resistance including Extended Spectrum Beta Lactamases (ESBL) among E. coli isolated from Kenyan children at hospital discharge. PLoS Negl Trop Dis 16: e0010283. DOI: 10.1371/journal.pntd.0010283.
van de Lagemaat M, Stockbroekx V, Geertsema-Doornbusch GI, Dijk M, Carniello V, Woudstra W, van der Mei HC, Busscher HJ, Ren Y. 2022. A comparison of the adaptive response of Staphylococcus aureus vs. Streptococcus mutans and the development of chlorhexidine resistance. Front Microbiol 13: 861890. DOI: 10.3389/fmicb.2022.861890.
Veilumuthu P, Christopher JG. 2022. Antimicrobial compounds produced by Streptomyces sp. VITGV01 against selected human pathogens. Res J Biotechnol 17 (12): 16-28. DOI: 10.25303/1712rjbt16028.
Viswapriya V, Kumari PS. 2022. Combating the emerging drug-resistant Pseudomonas aeruginosa by an antibiotic purified from the novel Streptomyces violascens strain vs. Intl J Pharm Sci Res 13 (10): 4062-4070. DOI: 10.13040/ijpsr.0975-8232.13(10).4062-70.
WHO. 2022. World Health Statistics 2022 (Monitoring health of the SDGs). http://apps.who.int/bookorders.
Xu J-H, Gu K-B, Zhang D-J, Li Y-G, Tian L. 2017. Ghanamycins A and B, two novel γ-butyrolactones from marine-derived Streptomyces ghanaensis TXC6-16. J Antibiot 70: 733-736. DOI: 10.1038/ja.2017.37.
Yang W, Liang G, Sun Y, Gong Z. 2021. Bioactive secondary metabolites from marine Streptomyces griseorubens f8: Isolation, identification and biological activity assay. J Mar Sci Eng 9 (9): 978. DOI: 10.3390/jmse9090978.