Analisis Variasi dan Filogenetik Keragaman Gen 16S rRNA pada Staphylococcus aureus Berdasarkan Data NCBI
DOI:
https://doi.org/10.29303/d3g8th53Kata Kunci:
Staphylococcus aureus, 16S rRNA, keragaman genetik, filogenetik, bioinformatikaAbstrak
Staphylococcus aureus merupakan bakteri patogen penting yang sering dianalisis menggunakan gen 16S rRNA karena gen ini memiliki wilayah konservatif yang stabil sekaligus daerah hipervariabel yang informatif untuk kajian filogenetik. Penelitian ini bertujuan untuk menganalisis validitas data, tingkat keragaman genetik, hubungan filogenetik, serta indikasi penyebaran geografis S. aureus berdasarkan sekuens gen 16S rRNA. Sebanyak 60 sekuens gen 16S rRNA yang berasal dari berbagai benua dianalisis menggunakan pendekatan bioinformatika. Hasil analisis menunjukkan bahwa seluruh sekuens memiliki panjang yang bervariasi namun masih berada dalam rentang yang layak untuk analisis filogenetik. Multiple sequence alignment memperlihatkan dominasi nukleotida konservatif dengan jumlah SNP dan situs variabel yang relatif sedikit, menandakan tingkat keragaman genetik yang rendah pada gen 16S rRNA S. aureus. Analisis filogenetik menggunakan metode Neighbor-Joining dengan 500 kali bootstrap menghasilkan empat klaster utama (A–D) dengan tingkat dukungan yang bervariasi, menunjukkan adanya hubungan evolusi yang berbeda antar isolat. Secara keseluruhan, hasil penelitian ini mengindikasikan bahwa gen 16S rRNA S. aureus bersifat relatif stabil dan mendukung penggunaannya sebagai penanda molekuler untuk studi filogenetik dan epidemiologi global.
Referensi
Acid, Y. D. A. Abdullatif. (2016). Daya Hambat Ekstrak Rimpang Kunyit (Curcuma domestica Val.) Terhadap Pertumbuhan Staphylococcus aureus dan Staphylococcus epidermidis Secara In Vitro. Program Studi D-IV Analis Kesehatan Fakultas Keperawatan dan Kesehatan Universitas Muhammadiyah Semarang. Journal of Clinical Investigation, 111(9), 1265-1273.
Akihary, C. V., & Kolondam, B. J. (2020). Pemanfaatan gen 16S Rrna sebagai Perangkat Identifikasi Bakteri untuk Penelitian-Penelitian di Indonesia. Pharmacon, 9(1), 16-22. https://doi.org/10.35799/pha.9.2020.27405
Alexandrov LB. Signatures of mutational processes in human cancer. Nature. 2013; 500:415–21.
Alyamani, N. M. (2024). Partial and complete sequence of small and large subunit ribosomal RNA genes, tRNA-Val gene in some species of family Labridae. Open Veterinary Journal, 14(12), 3336.
Arnold, B. J., Huang, I. T., & Hanage, W. P. (2022). Horizontal gene transfer and adaptive evolution in bacteria. Nature Reviews Microbiology, 20(4), 206-218.
Bacolla A, Cooper DN, Vasquez KM. Mechanisms of base substitution mutagenesis in cancer genomes. Genes. 2014;5:108–46
Balaban, M., Moshiri, N., Mai, U., Jia, X., & Mirarab, S. (2019). TreeCluster: Clustering biological sequences using phylogenetic trees. PloS one, 14(8), e0221068. Pertiwi, W., Judijanto, L., Apriansi, M., Suparningtyas, J. F., Lada, Y. G., Mahyuni, S., & Nuroniah, H. S. (2025). Bioteknologi: Teori dan Penerapan dalam Berbagai Bidang. PT. Sonpedia Publishing Indonesia.
Chakravorty, S., Helb, D., Burday, M., Connell, N., & Alland, D. (2007). A Detailed Analysis Of 16S Ribosomal RNA Gene Segments For The Diagnosis Of Pathogenic Bacteria. Journal of microbiological methods, 69(2), 330-339. https://doi.org/10.1016/j.mimet.2007.02.005
Clarridge III, J. E. (2004). Impact Of 16S rRNA Gene Sequence Analysis for Identification of Bacteria on Clinical Microbiology and Infectious Diseases. Clinical microbiology reviews. 17(4), 840-862. https://doi.org/10.1128/CMR.17.4.840-862.2004
Dewi, P. M. P., Besung, I. N. K., & Mahardika, I. G. N. K. (2015). Keragaman Spesies dan Genetik Bakteri Staphylococcus Pada Ikan Tuna dengan Analisis Sekuen 16s rRNA. Jurnal Veteriner, 16(3), 409-415.
Fernández, A., Segura-Alabart, N., & Serratosa, F. (2023). The multifurcating neighbor-joining algorithm for reconstructing polytomic phylogenetic trees. Journal of Molecular Evolution, 91(6), 773-779.
Johnston, P. R., Quijada, L., Smith, C. A., Baral, H. O., Hosoya, T., Baschien, C., & Townsend, J. P. (2019). A multigene phylogeny toward a new phylogenetic classification of Leotiomycetes. IMA fungus, 10(1), 1. https://doi.org/10.1186/s43008-019-0002-x
Kampmann, M. L., Børsting, C., Jepsen, A. H., Andersen, M. M., Aagreen, C. I., Poggiali, B., ... & Andersen, J. D. (2025). Preparing for shotgun sequencing in forensic genetics–Evaluation of DNA extraction and library building methods. Forensic Science International: Genetics, 76, 103234.
Katsonis, P., Koire, A., Wilson, S. J., Hsu, T. K., Lua, R. C., Wilkins, A. D., & Lichtarge, O. (2014). Single nucleotide variations: biological impact and theoretical interpretation. Protein Science, 23(12), 1650-1666.
Muzzi, A., & Donati, C. (2011). Population genetics and evolution of the pan-genome of Streptococcus pneumoniae. International Journal of Medical Microbiology, 301(8), 619-622.
Peker, N., Garcia-Croes, S., Dijkhuizen, B., Wiersma, H. H., van Zanten, E., Wisselink, G., & Couto, N. (2019). A Comparison of Three Different Bioinformatics Analyses of the 16S-23S rRNA Encoding Region for Bacterial Identification. Frontiers in microbiology, 10, 620. https://doi.org/10.3389/fmicb.2019.00620
Reller, L. B., Weinstein, M. P., & Petti, C. A. (2007). Detection and Identification of Microorganisms by Gene Amplification and Sequencing. Clinical infectious diseases, 44(8), 1108-1114. https://doi.org/10.1086/512818
Sabat, A. J., van Zanten, E., Akkerboom, V., Wisselink, G., van Slochteren, K., de Boer, R. F., & Kooistra-Smid, A. M. (2017). Targeted Next-Generation Sequencing of The 16S-23S rRNA Region for Culture-Independent Bacterial Identification-Increased Discrimination Of Closely Related Species. Scientific reports, 7(1), 3434. https://doi.org/10.1038/s41598-017-03458-6
Saha, O., Hossain, M. S., & Rahaman, M. M. (2020). Genomic exploration light on multiple origin with potential parsimony-informative sites of the severe acute respiratory syndrome coronavirus 2 in Bangladesh. Gene reports, 21, 100951.
Santosaningsih, D., Santoso, S., Setijowati, N., Rasyid, H. A., Budayanti, N. S., Suata, K., & Severin, J. A. (2018). Prevalence and Characterisation of Staphylococcus aureus Causing Community‐Acquired Skin and Soft Tissue Infections on Java and Bali, Indonesia. Tropical Medicine & International Health, 23(1), 34-44. https://doi.org/10.1111/tmi.13000
Sato, A., Yamaguchi, T., Hamada, M., Ono, D., Sonoda, S., Oshiro, T., & Tateda, K. (2019). Morphological and biological characteristics of Staphylococcus aureus biofilm formed in the presence of plasma. Microbial Drug Resistance, 25(5), 668-676. https://doi.org/10.1089/mdr.2019.0068
Severn, M. M., Williams, M. R., Shahbandi, A., Bunch, Z. L., Lyon, L. M., Nguyen, A., dan Horswill, A. R. (2022). The Ubiquitous Human Skin Commensal Staphylococcus Hominis Protects Against Opportunistic Pathogens. MBio, 13(3), e00930-22. https://doi.org/10.1128/mbio.00930-22
Srinivasan, R., Karaoz, U., Volegova, M., MacKichan, J., Kato-Maeda, M., Miller, S., & Lynch, S. V. (2015). Use of 16S rRNA Gene for Identification of a Broad Range of Clinically Relevant Bacterial Pathogens. PloS one, 10(2), e0117617. https://doi.org/10.1371/journal.pone.0117617
Tindi, M., Mamangkey, N. G. F., & Wullur, S. (2017). The Dna Barcode And Molecular Phylogenetic Analysis Several Bivalve Species From North Sulawesi Waters Based On Coi Gene. Jurnal Pesisir Dan Laut Tropis, 1(2), 32–38.
Turbawaty, D. K., Logito, V., & Tjandrawati, A. (2021). Methicillin-Resistant Staphylococcus aureus (MRSA) Patterns And Antibiotic Susceptibility in Surgical and Non-Surgical Patients in a Tertiary Hospital in Indonesia. Majalah Kedokteran Bandung. 53(3), 148-154. https://doi.org/10.15395/mkb.v53n3.2396
Větrovský, T., & Baldrian, P. (2013). The Variability of The 16S rRNA Gene In Bacterial Genomes and Its Consekuens for Bacterial Community Analyses. PloS one, 8(2), e57923. https://doi.org/10.1371/journal.pone.0057923
Yan, A., Kus, J. V., & Sant, N. (2025). The Staphylococcus aureus Complex: Implications fo the Clinical Microbiology Laboratory. Journal of Clinical Microbiology, e01276-24. https://doi.org/10.1128/jcm.01276-24
Yuan, H., Xu, J., Wang, Y., Li, Y., Hao, Y., Long, J., & Yang, H. (2025). The Global Antimicrobial Resistance Trends of Staphylococcus aureus and Influencing Factors. Microbiology Research, 16(6), 118.
Unduhan
Diterbitkan
Terbitan
Bagian
Lisensi
Hak Cipta (c) 2026 Muhamad Aditio Apriesta Suharto, Dwi Cantika Juliani Putri, Padila Oktavia Ramdani, Jhulia Dwi Armayan, Faturrahman, Sarkono
Artikel ini berlisensiCreative Commons Attribution-ShareAlike 4.0 International License.
