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All Journal Journal of Microbiology, Biotechnology and Conservation
Faturrahman
University of Mataram
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemistry Environmental Science Immunology & microbiology

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Analisis Bioinformatika GenblaCTX-M Pengkode β-Laktamase Spektrum Luas pada Klebsiella pneumoniae Menggunakan Data GenBank NCBI Dwi Sakila Ulfa; Gusti Ayu Niscari Dewi; Ira Firati Fionita; Faturrahman; Sarkono
Journal of Microbiology, Biotechnology and Conservation Vol. 2 No. 1 (2026): Journal of Microbiology, Biotechnology and Conservation (jMBC)
Publisher : Master’s Program in Biology, Faculty of Mathematics and Natural Sciences, University of Mataram

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.29303/6805v662

Abstract

Klebsiella pneumoniae is a short rod-shaped Gram-negative bacterium capable of fermenting lactose and various other carbohydrates, producing acid and gas. The blaCTX-M gene is one of the major genes responsible for β-lactam resistance in K. pneumoniae. This study aimed to analyze the genetic variation and phylogenetic relationships of the blaCTX-M gene in K. pneumoniae using nucleotide sequence data retrieved from the NCBI GenBank database. A total of 19 sequences representing isolates from different countries were aligned to identify nucleotide variations. The alignment results revealed genetic variation among the isolates, with most forming a closely related cluster indicating high sequence similarity. Eighteen isolates showed identical characteristics with minor variations, while one isolate, NG_048898, exhibited the highest number of nucleotide variations. A total of 168 nucleotide variations were identified, predominantly nonsynonymous substitutions, distributed throughout the nucleotide sequence. Phylogenetic analysis using the Neighbor-Joining method with the Kimura 2-parameter model supported the alignment results, showing a distinct branch for isolate NG_048898, suggesting a different evolutionary origin. These findings highlight the genetic diversity of the blaCTX-M gene in K. pneumoniae isolates and provide important insights into the distribution of β-lactamase genes, which are essential for understanding antibiotic resistance patterns.
Analisis Filogenetik Gen nosZ pada Bakteri Pseudomonas sebagai Denitrifikasi Nitrogen Berbahaya Berdasarkan Data Sekuens NCBI Inayatul Izzati; Maulida Karima; Nayla Qoni’Atun Sholehah; Faturrahman; Sarkono
Journal of Microbiology, Biotechnology and Conservation Vol. 2 No. 1 (2026): Journal of Microbiology, Biotechnology and Conservation (jMBC)
Publisher : Master’s Program in Biology, Faculty of Mathematics and Natural Sciences, University of Mataram

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.29303/cy1q1033

Abstract

The nosZ gene plays a crucial role in the reduction of nitrous oxide (N₂O) to dinitrogen (N₂), an environmentally benign form of nitrogen. However, the evolutionary diversity of this gene within the genus Pseudomonas has not been comprehensively investigated. This study aimed to analyze the phylogenetic relationships of the nosZ gene in Pseudomonas and to elucidate patterns of relatedness and clade differentiation associated with N₂O reduction capability within this bacterial group. Phylogenetic analysis was conducted using the Maximum Likelihood method based on nosZ nucleotide sequences obtained from the NCBI database. The results showed that the closest genetic relationships were observed among isolates belonging to the same species, including Pseudomonas lini (sp 18 and 19), P. brassicacearum (sp 6 and 7), P. grimontii (sp 16 and 17), and P. mandelii (sp 11 and 12), all of which exhibited a genetic distance of 0.00. This finding indicates a high level of sequence conservation, likely influenced by strong functional selective pressure and similar geographic origins. In contrast, the most distant genetic relationships were observed between P. mandelii (sp 11) and P. lini (sp 19) with a genetic distance of 0.5, as well as between P. brassicacearum and several other species with distances reaching up to 0.6. These results highlight significant evolutionary variation of the nosZ gene among Pseudomonas species.
Analisis Variasi dan Filogenetik Keragaman Gen 16S rRNA pada Staphylococcus aureus Berdasarkan Data NCBI Muhamad Aditio Apriesta Suharto; Dwi Cantika Juliani Putri; Padila Oktavia Ramdani; Jhulia Dwi Armayanti; Faturrahman; Sarkono
Journal of Microbiology, Biotechnology and Conservation Vol. 2 No. 1 (2026): Journal of Microbiology, Biotechnology and Conservation (jMBC)
Publisher : Master’s Program in Biology, Faculty of Mathematics and Natural Sciences, University of Mataram

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.29303/d3g8th53

Abstract

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.
Co-Authors Dwi Cantika Juliani Putri Dwi Sakila Ulfa Gusti Ayu Niscari Dewi Inayatul Izzati Ira Firati Fionita Jhulia Dwi Armayanti Maulida Karima Muhamad Aditio Apriesta Suharto Nayla Qoni’Atun Sholehah Padila Oktavia Ramdani Sarkono