Doctoral Program Graduate School of Life, Natural Science and Technology, Okayama University, Japan
RESEARCH, TEACHING, or OTHER INTERESTS
Molecular Biology
6
Scopus Publications
20
Scholar Citations
3
Scholar h-index
Scopus Publications
Comparative Genomic Analysis Identifies FleQ and GcbB as Virulence-Associated Factors in Pseudomonas syringae pv. tabaci Strains Muhammad Taufiq Hidayat, Kei Yoshioka, Takafumi Nishimura, Shuta Asai, Sachiko Masuda, Ken Shirasu, Nanami Sakata, Mikihiro Yamamoto, Yoshiteru Noutoshi, Kazuhiro Toyoda, Yuki Ichinose, Hidenori Matsui Molecular Plant Pathology, 2025 Pseudomonas syringae pv. tabaci (Pta) is an important plant pathogen, which causes wildfire disease in Nicotiana species. However, the genetic basis underlying strain‐level differences in virulence remains largely unresolved. To address this, we performed a comparative genomic analysis between a highly virulent strain Pta 6605 and a less virulent strain Pta 7375. Despite high overall genome similarity, we identified key single‐nucleotide polymorphisms, including premature stop‐codon mutations in seven open reading frames in Pta 7375. Notably, point mutations in two regulatory genes, such as fleQ , which encodes a transcription factor essential for flagellar biogenesis and biofilm formation, and gcbB , which encodes a GGDEF domain‐containing diguanylate cyclase responsible for cyclic dimeric guanosine monophosphate (c‐di‐GMP) synthesis, were implicated in virulence disparity. Functional analyses using deletion and locus replacement mutants in the Pta 6605 background revealed that the disruption of fleQ markedly reduced motility, flagellin production, c‐di‐GMP accumulation, biofilm formation and virulence level mirroring the Pta 7375 phenotype. The gcbB replacement mutant showed reduced disease symptom development, although c‐di‐GMP levels remained comparable to the Pta 6605 wild type. Locus replacement between strains confirmed that a point mutation in fleQ was the primary driver of reduced motility and flagellin expression in Pta 7375. These findings indicate that the reduced virulence of Pta 7375 is associated with impaired regulation of flagella‐related genes and disruption of the FleQ‐mediated c‐di‐GMP signalling, underscoring the value of comparative genomics in disentangling the complex regulatory networks that govern virulence in plant pathogens.
PCR Optimization for Polyketide Synthase (PKS) and Non-Ribosomal Peptide Synthetase (NRPS) Gene Detection in Actinomycetes Endah Prayekti, Muhammad Taufiq Hidayat, Devita Rahma Putri, Nur Syamsiatul Fajar Bio Web of Conferences, 2024 Actinomycetes are known as a group of antimicrobial-producing bacteria. This is supported by the presence of potential genes in actinomycetes bacteria. These genes include Polyketide Synthase (PKS) and Non-Ribosomal Peptide Synthetase (NRPS). Detection of these genes using PCR requires the optimum annealing temperature so that the detection process runs accurately. The purpose of this study was to determine the appropriate annealing temperature in the detection of PKS I, PKS II and NRPS genes in actinomycetes bacterial isolates. The study was carried out experimentally with varying annealing temperatures of 52°C and 55°C. The results showed that all three genes were detected at 52°C, while at 55°C the PKS I gene bands were faint, and no PKS II and NRPS gene bands were found. Based on the results obtained, a temperature of 52°C is a suitable temperature for the detection of PKS I, II and NRPS genes.
Effect of feed supplement modifications using keratinolytic bacteria on growth performance and meat chemical composition of domesticated quail ENDRY NUGROHO PRASETYO, MUHAMMAD TAUFIQ HIDAYAT, MAHARANI PERTIWI KOENTJORO Indian Journal of Animal Sciences, 2023 This study was carried out to determine a novel strategy for utilization of feather in poultry feed, along with the addition of immobilized keratinolytic Bacillus sp. SLII–1 as a supplement. Eighty male quails (day–old) were randomly divided into four diet groups, with each group receiving four different treatments. The results showed that Bacillus sp. SLII–I exhibited keratinolytic potential by increasing the protein solubility of feather meal in a liquid medium. The immobilization of Bacillus sp. SLII–I using 3% sodium alginate and 0.8% chitosan composition occurred at approximately 4.05×107 CFU/g, while the viable cells were maintained in acidic medium (pH 3.0) at around 3.95×107 CFU/g. Quails aged 19–33 days, fed with feather meal and Bacillus sp. SLII–1, demonstrated significantly higher weight gain and lower feed conversion ratio (FCR) as compared to those treated with feather meal without supplements. There were no significant differences in the values of dry matter, ash, and crude protein content of the meat among the quails in all the treatments. Therefore, feed supplemented with immobilized bacteria and feather waste can be utilized as an alternative diet for quails. This way, the use of feed materials can be reduced, and at the same time, chicken feather waste can be effectively utilized.
Development of Nested-PCR Assay for The Rapid Detection of Aspergillus fumigatus Maharani Pertiwi Koentjoro, Taufik Hidayat, Suprapto Maat, Abdul Hakim Zakkiy Fasya, Endry Nugroho Prasetyo Aip Conference Proceedings, 2023 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter Facebook Reddit LinkedIn Tools Icon Tools Reprints and Permissions Cite Icon Cite Search Site Citation Maharani Pertiwi Koentjoro, Taufik Hidayat, Suprapto Maat, Abdul Hakim Zakkiy Fasya, Endry Nugroho Prasetyo; Development of nested-PCR assay for the rapid detection of Aspergillus fumigatus. AIP Conference Proceedings 24 January 2023; 2634 (1): 020009. https://doi.org/10.1063/5.0111758 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAIP Publishing PortfolioAIP Conference Proceedings Search Advanced Search |Citation Search
Modified Spin Column-Based RNA Extraction Methods of Staphylococcus aureus using PureLink® RNA Mini Kit and Basic Laboratory Instrument Muhammad Taufiq Hidayat, Endry Nugroho Prasetyo Indonesian Journal of Medical Laboratory Science and Technology, 2021 RNA extraction is an important process before gene expression assessment at the transcriptomic level. RNA is a sensitive material to environmental factors such as temperature and contaminants, so the RNA extraction process generally requires sophisticated and expensive laboratory instruments. In this study, we extract RNA from Staphylococcus aureus bacteria using the PureLink® RNA Mini Kit. The instruments used in this study are basic instruments such as a hand homogenizer and non-thermal centrifuge. The results of RNA extraction were visualized using agarose gel electrophoresis. These results indicate that bacterial RNA extraction can be performed using the PureLink® RNA Mini Kit even with inexpensive basic laboratory instruments.
Immobilization of Bacillus sp. SLII-1 on chitosan-alginate hybrid material for promising feedstock supplement Muhammad Taufiq Hidayat, Maharani Pertiwi Koentjoro, Isdiantoni, Ida Ekawati, Endry Nugroho Prasetyo Aip Conference Proceedings, 2020 The increase in poultry meat production led to an increase in feed demand. On the other hand, poultry industry produces feather waste which composes 5-7 wt% of the total body weight. Feed diversification by utilizing feather waste can be an alternative to overcome the problem of the high price of feed and to reduce environmental waste. The use of feather as a feed has a disadvantage because of the low digestibility of feather waste. The strategy to increase the digestibility of feather waste is to deliver keratinolytic bacteria to poultry intestine using immobilization technique. The purpose of this study was to determine the sodium alginate and chitosan concentration of immobilant with the highest number of released cell in poultry digestive system simulation. Bacillus sp. SLII-I as keratinolytic bacteria was able to increase soluble protein in feather meal liquid medium by 117.69% (wt/v). The composition of sodium alginate (2% w/v) and chitosan (0,8% w/v) was the most effective in delivering bacteria to poultry intestine as much as 2.54x107 CFU per gram bead in digestive system simulation.
RECENT SCHOLAR PUBLICATIONS
In Silico Detection of Antimicrobial Resistance and Virulence Genes in Methicillin Resistant Staphylococcus aureus Clinical Isolates: A Comparative Genomics Approach MT Hidayat, E Prayekti, MA Romdloni, SA Syah BIOPENDIX: Jurnal Biologi, Pendidikan dan Terapan 13 (1), 7-13 , 2026 2026
Comparative Genomic Analysis Identifies FleQ and GcbB as Virulence‐Associated Factors in Pseudomonas syringae pv. tabaci Strains MT Hidayat, K Yoshioka, T Nishimura, S Asai, S Masuda, K Shirasu, ... Molecular Plant Pathology 26 (11), e70168 , 2025 2025
Detection of mecA Genes from Staphylococcus aureus Bacteria in Raw Cow Milk in the Surabaya Regional Farm AAP Lestari, EP Prayekti, MT Hidayat Jurnal Analis Medika Biosains (JAMBS) 11 (2), 132-138 , 2024 2024
NEW PRIMER DESIGN of MULTIPLEX POLYMERASE CHAIN REACTION (PCR) for DETECTION of Escherichia Coli and Salmonella Enterica in FOOD SAMPLE MT Hidayat, E Prayekti, YT Lukiyono, MA Romdhoni, DF Sari BIOPENDIX: Jurnal Biologi, Pendidikan dan Terapan 11 (1), 17-25 , 2024 2024
PCR Optimization for Polyketide Synthase (PKS) and Non-Ribosomal Peptide Synthetase (NRPS) Gene Detection in Actinomycetes E Prayekti, MT Hidayat, DR Putri, NS Fajar BIO Web of Conferences 117, 01041 , 2024 2024
Effect of feed supplement modifications using keratinolytic bacteria on growth performance and meat chemical composition of domesticated quail EN Prasetyo, MT Hidayat, MP Koentjoro Indian Journal of Animal Sciences 93 (10), 1015-1020 , 2023 2023 Citations: 1
Edukasi Kelor Antibakteri Herbal dan Pelatihan Teh Kelor untuk Warga Desa Simoangin MT Hidayat, E Prayekti, M Zamzam, YT Lukiyono, MA Romdloni Jurnal Pengabdian Masyarakat Indonesia 3 (4), 597-604 , 2023 2023
Antimicrobial Activity Test of Medicinal Plant Extract Using Antimicrobial Disc and Filter Paper MT Hidayat, MP Koentjoro, EN Prasetyo Bioscientist: Jurnal Ilmiah Biologi 11 (1), 456-464 , 2023 2023 Citations: 7
Development of nested-PCR assay for the rapid detection of Aspergillus fumigatus MP Koentjoro, T Hidayat, S Maat, AHZ Fasya, EN Prasetyo AIP Conference Proceedings 2634 (1), 020009 , 2023 2023 Citations: 1
Perbandingan Tiga Metode Isolasi DNA Asperigilus niger A Donastin, MP Koentjoro, MT Hidayat, EN Prasetyo Metamorfosa: Journal of Biological Science 9 (1), 69-78 , 2022 2022 Citations: 3
Studi Aktivitas Antibiotik Ekstrak Tanaman Obat Terhadap Ekspresi Gen Biosintesis Peptidoglikan (pbp2 dan MurA) Staphylococcus aureus MT Hidayat Institut Teknologi Sepuluh Nopember , 2022 2022
Modified Spin Column-Based RNA Extraction Methods of Staphylococcus aureus using PureLink® RNA Mini Kit and Basic Laboratory Instrument MT Hidayat, EN Prasetyo Indonesian Journal of Medical Laboratory Science and Technology 3 (2), 73-80 , 2021 2021 Citations: 7
Immobilization of Bacillus sp. SLII-1 on chitosan-alginate hybrid material for promising feedstock supplement MT Hidayat, MP Koentjoro, Isdiantoni, I Ekawati, EN Prasetyo AIP Conference Proceedings 2215 (1), 070004 , 2020 2020 Citations: 1
MOST CITED SCHOLAR PUBLICATIONS
Antimicrobial Activity Test of Medicinal Plant Extract Using Antimicrobial Disc and Filter Paper MT Hidayat, MP Koentjoro, EN Prasetyo Bioscientist: Jurnal Ilmiah Biologi 11 (1), 456-464 , 2023 2023 Citations: 7
Modified Spin Column-Based RNA Extraction Methods of Staphylococcus aureus using PureLink® RNA Mini Kit and Basic Laboratory Instrument MT Hidayat, EN Prasetyo Indonesian Journal of Medical Laboratory Science and Technology 3 (2), 73-80 , 2021 2021 Citations: 7
Perbandingan Tiga Metode Isolasi DNA Asperigilus niger A Donastin, MP Koentjoro, MT Hidayat, EN Prasetyo Metamorfosa: Journal of Biological Science 9 (1), 69-78 , 2022 2022 Citations: 3
Effect of feed supplement modifications using keratinolytic bacteria on growth performance and meat chemical composition of domesticated quail EN Prasetyo, MT Hidayat, MP Koentjoro Indian Journal of Animal Sciences 93 (10), 1015-1020 , 2023 2023 Citations: 1
Development of nested-PCR assay for the rapid detection of Aspergillus fumigatus MP Koentjoro, T Hidayat, S Maat, AHZ Fasya, EN Prasetyo AIP Conference Proceedings 2634 (1), 020009 , 2023 2023 Citations: 1
Immobilization of Bacillus sp. SLII-1 on chitosan-alginate hybrid material for promising feedstock supplement MT Hidayat, MP Koentjoro, Isdiantoni, I Ekawati, EN Prasetyo AIP Conference Proceedings 2215 (1), 070004 , 2020 2020 Citations: 1
In Silico Detection of Antimicrobial Resistance and Virulence Genes in Methicillin Resistant Staphylococcus aureus Clinical Isolates: A Comparative Genomics Approach MT Hidayat, E Prayekti, MA Romdloni, SA Syah BIOPENDIX: Jurnal Biologi, Pendidikan dan Terapan 13 (1), 7-13 , 2026 2026
Comparative Genomic Analysis Identifies FleQ and GcbB as Virulence‐Associated Factors in Pseudomonas syringae pv. tabaci Strains MT Hidayat, K Yoshioka, T Nishimura, S Asai, S Masuda, K Shirasu, ... Molecular Plant Pathology 26 (11), e70168 , 2025 2025
Detection of mecA Genes from Staphylococcus aureus Bacteria in Raw Cow Milk in the Surabaya Regional Farm AAP Lestari, EP Prayekti, MT Hidayat Jurnal Analis Medika Biosains (JAMBS) 11 (2), 132-138 , 2024 2024
NEW PRIMER DESIGN of MULTIPLEX POLYMERASE CHAIN REACTION (PCR) for DETECTION of Escherichia Coli and Salmonella Enterica in FOOD SAMPLE MT Hidayat, E Prayekti, YT Lukiyono, MA Romdhoni, DF Sari BIOPENDIX: Jurnal Biologi, Pendidikan dan Terapan 11 (1), 17-25 , 2024 2024
PCR Optimization for Polyketide Synthase (PKS) and Non-Ribosomal Peptide Synthetase (NRPS) Gene Detection in Actinomycetes E Prayekti, MT Hidayat, DR Putri, NS Fajar BIO Web of Conferences 117, 01041 , 2024 2024
Edukasi Kelor Antibakteri Herbal dan Pelatihan Teh Kelor untuk Warga Desa Simoangin MT Hidayat, E Prayekti, M Zamzam, YT Lukiyono, MA Romdloni Jurnal Pengabdian Masyarakat Indonesia 3 (4), 597-604 , 2023 2023
Studi Aktivitas Antibiotik Ekstrak Tanaman Obat Terhadap Ekspresi Gen Biosintesis Peptidoglikan (pbp2 dan MurA) Staphylococcus aureus MT Hidayat Institut Teknologi Sepuluh Nopember , 2022 2022
