Isolasi dan Identifikasi Molekuler Bakteri Salmonella Asal Tempe Dage Berdasarkan Gen 16S rRNA
DOI:
https://doi.org/10.33394/bioscientist.v13i4.18200Keywords:
Bakteri, patogen bawaan pangan, Salmonella, tempe dage, 16S rRNAAbstract
This study aimed to isolate Salmonella from tempe dage, particularly products sold in traditional markets in the Banyumas region, Central Java, and to identify the isolates through molecular analysis of the 16S rRNA gene. Isolation of Salmonella from dage samples was conducted using culture-based methods on several types of selective media specific for Salmonella. Identification was performed through biochemical characterization using the API 20E system and molecular analysis based on PCR amplification of the 16S rRNA gene. The resulting 16S rRNA sequences were subsequently analyzed using the BLAST tool available on the NCBI platform, and phylogenetic relationships were reconstructed with MEGA X. The study successfully obtained one bacterial isolate (TD.1), exhibiting transparent colonies with black centers on SSA medium. Biochemical tests including catalase activity, sugar fermentation, H₂S production, and citrate utilization showed positive results. Further identification using the API 20E system confirmed that isolate TD.1 belonged to the genus Salmonella. Molecular analysis of the 16S rRNA gene identified isolate TD.1 as Salmonella enterica. In conclusion, isolate TD.1, recovered from tempe dage was identified as Salmonella enterica. The presence of Salmonella enterica in dage highlights a potential health risk and underscores the need for improved food hygiene in traditional markets.
References
Abellan-Schneyder, I., Matchado, M. S., Reitmeier, S., Sommer, A., Sewald, Z., Baumbach, J., List, M., & Neuhaus, K. (2021). Primer, Pipelines, Parameters: Issues in 16S rRNA Gene Sequencing. MSphere, 6(1), 1–22. https://doi.org/10.1128/msphere.01202-20
Aguirre-garcia, Y. L., Nery-flores, S. D., Campos-muzquiz, L. G., Flores-gallegos, A. C., Palomo-ligas, L., & Alberto, J. (2024). Lactic Acid Fermentation in the Food Industry and Bio-Preservation of Food. Fermentation, 10(168). https://doi.org/ 10.3390/fermentation10030168
Akihary, C. V., & Kolondam, B. J. (2020). Utilization of the 16S rRNA gene as a bacterial identification device for research in Indonesia. Pharmacon, 9(1), 16–22.
Arbefeville, S. S., Timbrook, T. T., & Garner, C. D. (2024). Evolving strategies in microbe identification - a comprehensive review of biochemical, MALDI-TOF MS and molecular testing methods. Journal of Antimicrobial Chemotherapy, 79, 12–18. https://doi.org/10.1093/jac/dkae275
Azwar, S. M. (2022). Isolasi dan Karakterisasi Molekuler Gen 16S rRNA Bakteri Lipolitik Asal Limbah Kulit Biji Jambu Mete Isolation and Molecular Characterization of Lipolytic Bacterial 16S rRNA Gene from Cashew Nutshell Waste. Jurnal Sumberdaya HAYATI, 8(1), 20–26. https://journal.ipb.ac.id/index.php/sumberdayahayati
Baek, S. H., Lim, C. G., Park, J. Il, Seo, Y. B., & Nam, I. S. (2024). Investigation of Salmonella enteritidis Growth under Varying Temperature Conditions in Liquid Whole Egg: Proposals for Smart Management Technology for Safe Refrigerated Storage. Foods, 13(19). https://doi.org/10.3390/foods13193106
Balasubramanian, R., Im, J., Lee, J. S., Jeon, H. J., Mogeni, O. D., Kim, J. H., Rakotozandrindrainy, R., Baker, S., & Marks, F. (2019). The global burden and epidemiology of invasive non-typhoidal Salmonella infections. Human Vaccines and Immunotherapeutics, 15(6), 1421–1426. https://doi.org/10.1080/21645515.2018.1504717
Bhattacharyya, Roy, & Das. (2023). Overview on Old and New Biochemical Test for Bacterial Identification. Journal of Surgical Case Reports and Images, 6(5), 01–11. https://doi.org/10.31579/2690-1897/163
Bukin, Y. S., Galachyants, Y. P., Morozov, I. V., Bukin, S. V., Zakharenko, A. S., & Zemskaya, T. I. (2019). The effect of 16s rRNA region choice on bacterial community metabarcoding results. Scientific Data, 6, 1–14. https://doi.org/10.1038/sdata.2019.7
Chanamé Pinedo, L., Mughini-Gras, L., Franz, E., Hald, T., & Pires, S. M. (2022). Sources and trends of human salmonellosis in Europe, 2015–2019: An analysis of outbreak data. International Journal of Food Microbiology, 379(2). https://doi.org/10.1016/j.ijfoodmicro.2022.109850
Chaudhary, A., Solanki, S., & Gurjar, D. (2024). Biochemical characterization of Salmonella species isolated from calf diarrhoea. International Journal of Veterinary Sciences and Animal Husbandry, 9(1), 1034–1037.
Chen, W., & Wang, H. (2022). Phylogenetic Tree Selection by Testing Substitution Number in Clade. Diversity, 14(7). https://doi.org/10.3390/d14070543
Deng, X., Li, S., Xu, T., Zhou, Z., Moore, M. M., Timme, R., Zhao, S., Lane, C., Dinsmore, B. A., Weill, F. X., & Fields, P. I. (2025). Serotype interpretation from DNA sequence data. Applied and environmental Microbiology, 91(3).
Ehuwa, O., Jaiswal, A. K., & Jaiswal, S. (2021). Salmonella, food safety and food handling practices. Foods, 10(5), 1–16. https://doi.org/10.3390/foods10050907
Elsyaningrat, I. G. A. I. G., Pinatih, K. J. P., Fatmawati, N. N. D., & Darwinata, A. E. (2022). Prevalensi cemaran patogen Salmonella pada daging babi yang dijual di Pasar Tradisional di Kota Denpasar. Intisari Sains Medis, 13(2), 328–334. https://doi.org/10.15562/ism.v13i2.1381
Eshananda, Y., Fikriyya, N., & Fadlilah, S. H. (2023). Deteksi Molekuler Bakteri Patogen pada Makanan Fermentasi Tempe Dage berdasarkan marka gen 16S rRNA. Agropross : National Conference Proceedings of Agriculture, 591–598. https://doi.org/10.25047/agropross.2023.491
Evangelopoulou, G., Burriel, A. R., & Solomakos, N. (2024). Distinctive Culture Expressions of Enterobacteria Interfering with Isolation of Salmonella spp. during the Application of the Recommended ISO 6579-1:2017. Applied Sciences (Switzerland), 14(3). https://doi.org/10.3390/app14030953
Ferrari, R. G., Rosario, D. K. A., Cunha-Neto, A., Mano, S. B., Figueiredo, E. E. S., & Conte-Juniora, C. A. (2019). Worldwide epidemiology of Salmonella serovars in animal-based foods: A meta-analysis. Applied and Environmental Microbiology, 85(14), 1–21. https://doi.org/10.1128/AEM.00591-19
Grinevich, D., Harden, L., Thakur, S., Callahan, B., Grinevich, D., Harden, L., Thakur, S., & Callahan, B. (2024). Serovar-level identification of bacterial foodborne pathogens from full-length 16S rRNA gene sequencing. Computational Biology, 9(3), 1–18.
Hafezi, A., & Khamar, Z. (2024). The Method and Analysis of Some Biochemical Tests Commonly Used for Microbial Identification: A Review. Comprehensive Health and Biomedical Studies, 3(2). https://doi.org/10.5812/chbs-160199
Hashemi, M., Erfani, A., Asadi Touranlou, F., Doustinouri, M., Shahraki, A., & Afshari, A. (2025). Identification of Salmonella Enteritidis, Salmonella Typhimurium, Bacillus cereus, Bacillus subtilis, and Clostridium perfringens in hospital food. Revista Argentina de Microbiologia, 57(1), 78–85. https://doi.org/10.1016/j.ram.2024.11.005
Ibrahim, G. M., & Morin, P. M. (2018). Salmonella serotyping using whole genome sequencing. Frontiers in Microbiology, 9(12), 1–8. https://doi.org/10.3389/fmicb.2018.02993
Id, R. C., Nguyen-viet, H., Tum, S., Unger, F., Lindahl, J., Grace, D., Ty, C., Koam, S., Sina, V., Sokchea, H., Pov, S., Heng, T., Phirum, O., & Dang-xuan, S. (2022). Experimental cross-contamination of chicken salad with Salmonella enterica serovars Typhimurium and London during food preparation in Cambodian households. PLoS ONE, 1, 1–18. https://doi.org/10.1371/journal.pone.0270425
Inayah, M. N., Lestari, Y., & Meryandini, A. (2022). Community of Soil Actinobacteria in PTPN VI Oil Palm Plantation Jambi (Sumatra, Indonesia) Based on Amplicon Sequencing of 16S rRNA Gene. HAYATI Journal of Biosciences, 29(3), 389–398. https://doi.org/10.4308/hjb.29.3.389-398
Johnson, J. S., Spakowicz, D. J., Hong, B. Y., Petersen, L. M., Demkowicz, P., Chen, L., Leopold, S. R., Hanson, B. M., Agresta, H. O., Gerstein, M., Sodergren, E., & Weinstock, G. M. (2019). Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis. Nature Communications, 10(1), 1–11. https://doi.org/10.1038/s41467-019-13036-1
Kankanawadi, R., Awati, B., & Kage, S. (2022). Isolation, cultural and morphological characterization of Salmonella Spp. from diarrhoeic cases of Pigs. The Pharma Innovation Journal, 11(10), 1176–1181.
Noer, S. (2021). Identifikasi Bakteri secara Molekular Menggunakan 16S rRNA. EduBiologia: Biological Science and Education Journal, 1(1), 1. https://doi.org/10.30998/edubiologia.v1i1.8596
Nurjanah, S., Rahayu, W. P., Dewanti-Hariyadi, R., Asthiti, N. G. A. M. W., & Melati, R. P. (2021). Simpleks Dan Multipleks Pre-Enrichment-PCR Untuk Deteksi Salmonella Enteritidis DAN Typhimurium Pada Karkas Ayam. Jurnal Teknologi Dan Industri Pangan, 32(1), 148–156. https://doi.org/10.6066/jtip.2021.32.2.148
Omar, D., Al-Ashmawy, M., Ramadan, H., & El-Sherbiny, M. (2018). Occurrence and PCR identification of Salmonella spp. from milk and dairy products in Mansoura, Egypt. International Food Research Journal, 25(1), 446–452.
Pop, O. L., Ciont, C., Gabianelli, R., Coldea, T. E., Pop, C. R., Mudura, E., Min, T., Rangnoi, K., Yamabhai, M., Vlaic, R., Mureșan, C., & Suharoschi, R. (2024). Deciphering contaminants and toxins in fermented food for enhanced human health safeguarding. Comprehensive Reviews in Food Science and Food Safety, 23(5). https://doi.org/10.1111/1541-4337.13428
Ranjbar, R., Mojtaba, S., Mehrabi, A., Sarshar, M., Najafi, A., & Soruri, R. (2017). Simultaneous Molecular Detection of Salmonella enterica Sero. Iran J Public Health, 46(1), 103–111. http://ijph.tums.ac.ir
Risdayanti, R., Latif, U. T. A., & Wirawan, H. P. (2023). Deteksi keberadaan bakteri pengkontaminasi pangan Salmonella sp. pada telur. Filogeni: Jurnal Mahasiswa Biologi, 3(3), 117–121. https://doi.org/10.24252/filogeni.v3i3.29811
Rizki, R. P., Arifin, M. Z., & Aini, I. (2022). Identification of Salmonella Sp Bacterial Contamination in Broiler Chicken at Pon Market, Jombang Regency. Medicra (Journal of Medical Laboratory Science/Technology), 5(1), 6–10. https://doi.org/10.21070/medicra.v5i1.1621
Santos, P. D. M., Widmer, K. W., & Rivera, W. L. (2020). PCR-based detection and serovar identification of Salmonella in retail meat collected from wet markets in Metro Manila, Philippines. PLoS ONE, 15(9), 1–17. https://doi.org/10.1371/journal.pone.0239457
Sayed, R., Ewida, R. M., & Sayed, M. (2023). Isolation and molecular identification of salmonella from fermented foods. Journal of Applied Molecular Biology, 1(1), 73–82. https://doi.org/10.21608/jamb.2023.218073.1006
Shoaib, M., Muzammil, I., Hammad, M., Bhutta, Z. A., & Yaseen, I. (2020). A Mini-Review on Commonly used Biochemical Tests for Identification of Bacteria. International Journal of Research Publications, 54(1). https://doi.org/10.47119/ijrp100541620201224
Sukmawati, S., Ratna, R., Sipriyadi, & Yunita, M. (2023). Characterization and molecular identification of bacteria from mackerel bekasam in Sorong City, Southwest Papua Province, Indonesia. Biodiversitas, 24(9), 4967–4977. https://doi.org/10.13057/biodiv/d240940
Turki, Y., Mehri, I., Khessairi, A., Agrebi, K., Hassen, A., & Ouzari, H. (2013). Identification of three related genera, Salmonella , Citrobacter and Proteus using API 20E, 16S-23S rDNA intergenic transcribed spacer fingerprinting and 16S rDNA sequencing. Academic Journals, 7(29), 3874–3884. https://doi.org/10.5897/AJMR2013.5466
Vakili, S., Haeili, M., Feizi, A., Moghaddasi, K., Omrani, M., Ghodousi, A., & Cirillo, D. M. (2025). Whole-genome sequencing-based characterization of Salmonella enterica Serovar Enteritidis and Kentucky isolated from laying hens in northwest of Iran, 2022–2023. Gut Pathogens, 17(1). https://doi.org/10.1186/s13099-025-00679-3
Wicaksono, W. A., Akinyemi, O. E., Wassermann, B., Bickel, S., Suwanto, A., & Berg, G. (2024). Traditionally produced tempeh harbors more diverse bacteria with more putative health-promoting properties than industrially produced tempeh. Food Research International, 196(9), 115030. https://doi.org/10.1016/j.foodres.2024.115030
Wotzka, S. Y., Nguyen, B. D., & Hardt, W. D. (2017). Salmonella Typhimurium Diarrhea Reveals Basic Principles of Enteropathogen Infection and Disease-Promoted DNA Exchange. Cell Host and Microbe, 21(4), 443–454. https://doi.org/10.1016/j.chom.2017.03.009
Wulan Agus Utami, A., Sari, D. D., Nirmalasari, Roza Sani Aidah, Rusdi, & Sari Utami Hidayati. (2025). Identification of Salmonella sp. bacteria Using ISO 6579-1:2017 Method for Frozen Salmon (Salmo salar) Products. Journal Of Biology Education Research (JBER), 6(1), 1–9. https://doi.org/10.55215/jber.v6i1.6
Yang, X., Wu, Q., Zhang, J., Huang, J., Chen, L., Wu, S., Zeng, H., Wang, J., Chen, M., Wu, H., Gu, Q., & Wei, X. (2019). Prevalence, bacterial load, and antimicrobial resistance of salmonella serovars isolated from retail meat and meat products in China. Frontiers in Microbiology, 10(9), 1–9. https://doi.org/10.3389/fmicb.2019.02121
Zahin, T., Abrar, M. H., Jewel, M. R., Tasnim, T., Bayzid, M. S., & Rahman, A. (2025). An alignment-free method for phylogeny estimation using maximum likelihood. BMC Bioinformatics, 26(1). https://doi.org/10.1186/s12859-025-06080-w
Zapa, A., Sokolowska, B., Bryla, M. (2022). Role of Lactic Acid Bacteria in Food Preservation and Safety. Foods, 11(1283), 1–17. https://doi.org/10.3390/foods11091283
Downloads
Published
How to Cite
Issue
Section
License
Copyright (c) 2025 Mazidah Noer Inayah, Suci Indah Budiarti, Rahayu Wulan
This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.
