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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.
Analisis Hubungan Kekerabatan Famili Felidae (Ordo Karnivora; Kelas Mamalia) Berdasarkan Sekuens Gen Cytochrome-B (CytB) Mitokondria Fatahillah Ardhani; Ida Ayu Dewi Lola Valastri; Khusnul Khotimah; Faturrahman
Journal of Microbiology, Biotechnology and Conservation Vol. 2 No. 2 (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/v6twrz55

Abstract

Species identification within the family Felidae is often challenged by overlapping morphological characteristics resulting from hybridization, necessitating the use of genetic approaches. This study aimed to analyze the phylogenetic relationships and evolutionary history of 40 Felidae species based on mitochondrial Cytochrome b (CytB) gene sequences. This in silico study utilized secondary data obtained from GenBank, which were analyzed using MEGA 12 for sequence alignment, nucleotide composition analysis, and phylogenetic tree reconstruction using the Maximum Likelihood method with 1,000 bootstrap replicates, followed by validation using DrPhylo. The results showed a predominance of transition mutations, with a high R ratio (9), as well as significant codon usage bias. Phylogenetic reconstruction divided the family Felidae into eight major clades supported by high bootstrap values, namely Panthera, Neofelis, Pardofelis, Prionailurus, Lynx, Leopardus, Felis, and a combined Puma group. The genus Otocolobus was identified as the oldest lineage, diverging earliest from the other lineages. The M-Grid test confirmed the validity of the major clade groupings, with confidence levels approaching 1.00. It can be concluded that the CytB gene is an effective and reliable genetic marker for phylogenetic studies of the family Felidae.
Analisis In Silico Tiga Varian of Uncertain Significance (VUS) pada Gen BRCA1 melalui Pendekatan BLASTp, Multiple Sequence Alignment, dan Filogenetik Fathiya Najwa Aziza; Fernanda Nathalien Haribu Peramu; Maeizatul Khusni Qamar; Faturrahman; Sarkono
Journal of Microbiology, Biotechnology and Conservation Vol. 2 No. 2 (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/ewwv1018

Abstract

The BRCA1 gene plays a critical role in maintaining genomic stability through DNA damage repair; therefore, mutations in this gene may increase the risk of breast and ovarian cancers. Numerous novel variants identified through sequencing are classified as Variants of Uncertain Significance (VUS), referring to variants whose biological effects remain undetermined. This study evaluated the potential pathogenicity of three BRCA1 VUSs using an in silico approach based on comparative protein sequence analysis. Three variants—p.Tyr1863Cys, p.Ser1180Arg, and p.Thr37Pro—were selected to represent mutations located in the C-terminus, central region, and N-terminus (RING domain), respectively. Wild-type Homo sapiens and mammalian ortholog protein sequences were retrieved from UniProt and aligned using MEGA to assess residue conservation, complemented by phylogenetic analysis to provide an evolutionary context. BLASTp was employed to assess sequence similarity and the homologous relationship between human BRCA1 and its orthologs. The results revealed distinct patterns of residue conservation: p.Tyr1863Cys occurred at a residue with low conservation, p.Ser1180Arg at a highly conserved residue, and p.Thr37Pro at a completely conserved residue within the RING domain. Integration of evolutionary conservation, domain localization, and changes in the chemical properties of the substituted residues indicated that p.Thr37Pro had the highest potential pathogenicity, followed by p.Ser1180Arg and p.Tyr1863Cys. All findings are predictive and require further experimental validation.
Co-Authors Dwi Cantika Juliani Putri Dwi Sakila Ulfa Fatahillah Ardhani Fathiya Najwa Aziza Fernanda Nathalien Haribu Peramu Gusti Ayu Niscari Dewi Ida Ayu Dewi Lola Valastri Inayatul Izzati Ira Firati Fionita Jhulia Dwi Armayanti Khusnul Khotimah Maeizatul Khusni Qamar Maulida Karima Muhamad Aditio Apriesta Suharto Nayla Qoni’Atun Sholehah Padila Oktavia Ramdani Sarkono