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All Journal HAYATI Journal of Biosciences Jurnal Ilmu Pertanian Indonesia Microbiology Indonesia Biota: Jurnal Ilmiah Ilmu-Ilmu Hayati Indonesian Journal of Biotechnology Biology, Medicine, & Natural Product Chemistry Jurnal Sumberdaya Hayati Makara Journal of Science Jurnal Natural Bioma : Jurnal Ilmiah Biologi Berita Biologi
Rika Indri Astuti
Departemen Biologi, Fakultas Matematika Dan Ilmu Pengetahuan Alam, Institut Pertanian Bogor, Kampus Darmaga IPB, Bogor 16680
Agriculture, Biological Sciences & Forestry Astronomy Biochemistry, Genetics & Molecular Biology Chemistry Earth & Planetary Sciences Education Energy Immunology & microbiology Materials Science & Nanotechnology Medicine & Pharmacology Neuroscience Physics Public Health

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Detection and Cloning of a Gene Involved in Zwitermicin A Synthesis from Plant Growth Promoting Rhizobacteria of Bacillus sp CR64 Wahyudi, Aris Tri; Astuti, Rika Indri; Mubarik, Nisa Rachmania; Faulina, Sarah Asih
Indonesian Journal of Biotechnology Vol 15, No 1 (2010)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (625.609 KB)

Abstract

Utilization of soil bacteria as biocontrol agent is becoming popular due to its valuable and effective mechanisms to suppress plant pathogenic microbes. We have previously isolated Bacillus sp, designated as Bacillus sp CR64, which exhibited effective plant growth promoting and antifungal activities. In this study, CR64 was examined in inhibiting the growth of Rhizoctonia solani, the causing agent of root rot disease. Partial sequence analysis of 16S rRNA gene revealed that this isolate similar with Bacillus cereus (94%). Furthermore, a gene designated zmaR was detected by means of specific amplification of DNA fragment approximately 950 bp. This fragment was then cloned onto pCRII-TOPO (3.9 kb) and sequenced using DNA sequencer ABI PRISM 310. Sequence analysis revealed that it had highest homology with the ZmaR protein (89% identity; 90% similarity) of B. thuringiensis serovar kurstaki (AAF82729.2). Alignment analysis with other ZmaR sequences from other antibiotic-producing Bacilli exhibited an almost fully conserved region within ZmaR sequences.Key words : PGPR, Bacillus sp CR64, Zwitermicin A, Cloning, Antifungal.
Metagenomic Analysis of Bacteria Phylum Firmicutes and Bacteroidetes in Women with Type 2 Diabetes Zulhaerati Zulhaerati; Sri Budiarti; Rika Indri Astuti
HAYATI Journal of Biosciences Vol. 26 No. 3 (2019): July 2019
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (365.115 KB) | DOI: 10.4308/hjb.26.3.110

Abstract

Diabetes mellitus (DM) is a serious health problem in Indonesia. Type 2 diabetes is a metabolic disease which primarily caused by obesity-linked insulin resistance. There is a link between insulin resistance and bacterial populations in the gut. Therefore, the aims of this study was to analyze composition of bacteria belong to the phylum Firmicutes and Bacteroidetes in women with type 2 diabetes and non-diabetic persons as control. The study included five female adults type 2 diabetes patients and five healthy controls. The bacteria composition was analyzed for abundance by denaturing gradient gel electrophoresis (DGGE). Metagenomic analysis based on 16S rRNA gene was represented by 12 DGGE bands. The twelve respective bands showed the similarity ranging from 77 up to 98%. Diversity of microbial composition in women type 2 diabetes was represented by five DGGE bands are Bacteroides fragilis, Bacteroides vulgatus, uncultured Bacteroides sp. clone Lb4eF4, uncultured bacterium clone 16sms90-5g05, and uncultured bacterium clone Malaga 1F14. Four DGGE bands in women healthy controls are closely related to uncultured bacterium isolate DGGE gel band Eub42, uncultured bacterium isolate DGGE gel band K115, uncultured bacterium clone HFV04255, and Enterococcus sp. the finding shows bacterial species belong to the phylum Bacteroidetes was mostly found in women diabetic group, while those belong to the phylum Firmicutes was mostly found in healthy controls.
Antioxidant Activity of Endophytic Bacteria Derived from Hoya multiflora Blume Plant and Their Cellular Activities on Schizosaccharomyces pombe Nabila Tsoerayya Gustia Pudjas; Nisa Rachmania Mubarik; Rika Indri Astuti; Lisdar I Sudirman
HAYATI Journal of Biosciences Vol. 29 No. 2 (2022): March 2022
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.29.2.214-221

Abstract

Endophytic bacteria isolated from plant tissues can produce the same secondary metabolites as their host plants. One of the metabolites that the bacteria can produce is antioxidants. This research aimed to analyze and measure the antioxidant activities of two endophytic bacteria, i.e. Bacillus siamensis HMB1 and Bacillus aryabhattai HMD4 cultures, derived from Hoya multiflora Blume plant, a tropical epiphytic plant species that grows in Indonesia, and to identify their cellular effects on Schizosaccharomyces pombe. The active compounds went through extraction process, and the antioxidant activities were measured, the extracts went under phytochemical analysis, and their phenol and flavonoid contents were measured. In vitro analysis was carried out using S. pombe. The results of this research indicated that both cultures had antioxidant activities, where HMB1 showed the highest IC50 value (51.18 mg/ml) among all. In vitro analysis indicated that HMD4 bacterial crude extract in 250 ppm concentration showed the highest resistance effect and significantly enhanced S. pombe growth. In addition, the results of the LC-MS analysis suggested that a total of 14 compounds potentially had antioxidant activity.
Skrining dan Identifikasi Bakteri Laut Penghasil Enzim Selulase yang Berasosiasi dengan Spons Rika Indri Astuti; Yohanes Bernadino Putera Saju; Dina Aribah; Aris Tri Wahyudi
Jurnal Ilmu Pertanian Indonesia Vol. 27 No. 1 (2022): Jurnal Ilmu Pertanian Indonesia
Publisher : Institut Pertanian Bogor

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.18343/jipi.27.1.70

Abstract

Marine bacteria associated with sponges can be used as a source of new enzymes, especially cellulase which are potentially used for various industries. The aim of this study was to screen and identify the cellulolytic bacteria associated with sponges. A total of 38 isolates have been successfully isolated from sponges Aaptos sp., Euryspongia sp., and Haliclona sp. by a spread plate method. Amongst 38 isolates, 14 (37%) showed cellulolytic activities in carboxy methyl cellulose (CMC) medium with a cellulolytic index ranging from 0.31 to 1.63. The three highest cellulolytic index was exhibited by bacterial isolates coded Y.5.10, Y.5.11, and Y.40.6. Isolates Y.5.10, Y.5.11, and Y.40.6 showed cellulolytic activity of 0.0053 U/mL; 0.0083 U/mL; and 0.0124 U/mL, respectively, as were tested by spectrophotometry. The highest specific enzymatic activity was showed by isolate Y.40.6 with a value of 0.3391 U/mg. Based on 16S rRNA gene, isolate Y.5.10, Y.5.11, and Y.40.6 were highly similar to (similarity ≥ 99%) Bacillus sp., B. subtilis, and B. cereus, respectively. Keywords: cellulase, isolation, sponge-associated bacteria, 16S rRNA
Seleksi, Karakterisasi Morfologi, dan Identifikasi Aktinobakteri Penghasil Mananase Asal Hutan Tanah Jambi untuk Produksi Mananoligosakarida Rahayu Wulan; Rika Indri Astuti; Yaya Rukayadi; Sri Estuningsih; Anja Meryandini
Jurnal Ilmu Pertanian Indonesia Vol. 27 No. 2 (2022): Jurnal Ilmu Pertanian Indonesia
Publisher : Institut Pertanian Bogor

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.18343/jipi.27.2.279

Abstract

As the world's largest producer of crude palm oil, Indonesia also produces high palm kernel cake (PKC) by-products. PKC has a high mannan content, so it can be used to produce prebiotic mannan-oligosaccharides (MOS). Enzymatic MOS production can be carried out using actinobacterial mannanase's microbiological approach. The HJ45B-1 isolate was the best isolate, with a peak enzyme production of 0,338 U/mL on the 10th day of incubation. The mannanase enzyme was stable in storage at 27°C. MOS production using 1% PKC substrate produced MOS with the best degree of polymerization (2-4) with incubation for 1-3 hours. Morphological characteristics and molecular identification based on the 16S rRNA gene indicated that the HJ45B-1 isolate was Streptomyces spp. Keywords: actinobacteria, mannanase, mannan-oligosaccharides, palm kernel cake, Streptomyces
Detection and Cloning of a Gene Involved in Zwitermicin A Synthesis from Plant Growth Promoting Rhizobacteria of Bacillus sp CR64 Aris Tri Wahyudi; Rika Indri Astuti; Nisa Rachmania Mubarik; Sarah Asih Faulina
Indonesian Journal of Biotechnology Vol 15, No 1 (2010)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (625.609 KB) | DOI: 10.22146/ijbiotech.7818

Abstract

Utilization of soil bacteria as biocontrol agent is becoming popular due to its valuable and effective mechanisms to suppress plant pathogenic microbes. We have previously isolated Bacillus sp, designated as Bacillus sp CR64, which exhibited effective plant growth promoting and antifungal activities. In this study, CR64 was examined in inhibiting the growth of Rhizoctonia solani, the causing agent of root rot disease. Partial sequence analysis of 16S rRNA gene revealed that this isolate similar with Bacillus cereus (94%). Furthermore, a gene designated zmaR was detected by means of specific amplification of DNA fragment approximately 950 bp. This fragment was then cloned onto pCRII-TOPO (3.9 kb) and sequenced using DNA sequencer ABI PRISM 310. Sequence analysis revealed that it had highest homology with the ZmaR protein (89% identity; 90% similarity) of B. thuringiensis serovar kurstaki (AAF82729.2). Alignment analysis with other ZmaR sequences from other antibiotic-producing Bacilli exhibited an almost fully conserved region within ZmaR sequences.Key words : PGPR, Bacillus sp CR64, Zwitermicin A, Cloning, Antifungal.
Ethanol Productivity of Ethanol-Tolerant Mutant Strain Pichia kudriavzevii R-T3 in Monoculture and Co-culture Fermentation with Saccharomyces cerevisiae Nurfadhilla Rahmadhani; Rika Indri Astuti; Anja Meryandini
HAYATI Journal of Biosciences Vol. 29 No. 4 (2022): July 2022
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.29.4.435-444

Abstract

We previously developed ethanol-tolerant P. kudriavzevii R-T3 (P.ku R-T3) mutant from its parental strain P.ku R-WT by evolutionary adaptation method. Hence, we further analyze the ethanol productivity of the particular isolates in a monoculture and co-culture with industrial yeast Saccharomyces cerevisiae BY4741 at various inoculum ratio. Based on the spot assay, R3 mutant yeast showed better cell viability under 10% ethanol stress than the wild type, potentially due to the high expression level of PKINO1 gene involved in the synthesis of inositol. In the monoculture fermentation, S. cerevisiae could use glucose, while P.ku could use mixed glucose and xylose as carbon sources for ethanol fermentation. P.ku R-T3 performed the most potential ethanol kinetics parameters, including the highest ethanol production (10.10 g/L), ethanol productivity (0.21 g/L/h), and fermentation efficiency (84.36%). Upscaling the inoculum of P.ku R-T3 by ten times resulted in 10% higher ethanol production. However, the highest substrate utilization rate did not indicate an increase in ethanol production. Indeed, P.ku R-T3 showed a low mixed substrate use but produced higher ethanol production than S. cerevisiae, as much as 21-31%, depending on the initial inoculum. Interestingly, the co-culture of P.ku R-T3 and BY4741 did not substantially produce higher ethanol production than the monoculture technique. About 30% reduction of ethanol production was found by co-culturing BY4741 with P.ku R-T3 than P.ku R-T3 alone. Taken together, the monoculture fermentation of P.ku R-T3 remains the promising fermentation technique than that of the co-culture with industrial yeast S. cerevisiae.
Characterization of Exon and Intron of Defensin 1 Gene in Apis cerana and Apis dorsata Alfiyan, Achmad; Raffiudin, Rika; Astuti, Rika Indri
Makara Journal of Science Vol. 23, No. 3
Publisher : UI Scholars Hub

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Abstract

Honey bee defensin 1 gene belongs to the class of immunity genes in this social insect. The peptide acts as a defensive mechanism against infections caused by Gram-positive bacteria. The aim of this study was to characterize exon 2, intron 2, and exon 3 of defensin 1 gene in both the Indonesian honey bees Apis cerana and A. dorsata. First, defensin 1 genes of A. cerana and A. dorsata were sequenced, after which a bioinformatic analysis was conducted. The amplified length of these defensin 1 genes of A. cerana and A. dorsata were 479 and 458 bp, respectively, and their putative amino acid sequences comprised 66 and 65 amino acids, respectively, with 6 cysteine residues. The cysteine residues formed a disulfide bond and then linked the three domains in the defensin peptide with each other, thereby allowing the lysis of the bacterial membrane through pore formation. Intron 2 of the defensin gene demonstrated nucleotide variations between A. cerana from Indonesia and that from Korea and between A. dorsata from Indonesia and that from Malaysia; the latter species also demonstrated variations in exon 3. Phylogenetic tree topology of the bee, which was constructed based on defensin 1 gene, was compatible with a previous study showing that A. cerana and A. dorsata are more closely related to A. mellifera than to A. florea.
Yeasts Isolated from Traditional Brem Bali Show Stress Tolerance Phenotype against Fermentation-Related Stresses Lenka, Audria Bayu; Astuti, Rika Indri; Listiyowati, Sri
Makara Journal of Science Vol. 25, No. 1
Publisher : UI Scholars Hub

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Abstract

The search for microbes, primarily yeasts with unique characters such as the tolerance against fermentation-related-stresses, is gaining significant interest nowadays. Traditionally made alcoholic beverages can be used as sources for such yeasts, given that during fermentation and storage, microbes may develop stress tolerance responses leading to naturally stress-tolerant yeast strains. In this study, we used an alcoholic beverage, that is, Brem Bali, as the source of potential yeast isolates. We isolated nine yeast isolates from two traditional Brem Bali products. All isolates showed tolerance against high glucose stress (40–50%) and sensitivity against high-temperature stress (37–50 °C). Notably, isolate BT5 showed tolerance phenotype against ethanol stress (up to 12.5%). Notably, the ethanol stress tolerance phenotype shown by isolate BT5 was unlikely correlated to the ability of the isolates in combating other stresses. Based on the internal transcribed spacer sequence, isolates BT2, BT5, and BT6 shared high similarity with Wickerhamomyces anomalus (98%). Further approaches may be needed to clarify the identity of these isolates. Based on our study, isolate BT5 bears potential as a fermentation agent based on its ability to combat high glucose and ethanol stresses.
Diversitas Pangan Fermentasi Berbasis-Susu di Indonesia dan Kandungan Gizinya Firyal Noviatanti Nabilah; Sri Listiyowati; Rika Indri Astuti
Jurnal Ilmu Pertanian Indonesia Vol. 27 No. 4 (2022): Jurnal Ilmu Pertanian Indonesia
Publisher : Institut Pertanian Bogor

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.18343/jipi.27.4.552

Abstract

Indonesia has abundant and diverse food commodities, including fermented food. However, metadata analysis about the diversity of fermented foods has not been reported. In addition, a comparison of the nutritional content of milk-based fermented foods is also not yet available. Therefore, this study aims to reveal the diverse status of fermented foods, to determine the nutritional content, especially of fermented milk-based foods, namely dangke, and their comparisons between milk-based fermented products. The research method included literature study, making dangke, proximate analysis of dangke, and statistical data analysis. Literature studies show that fermented foods and beverages in Indonesia were most reported in 2017, 2018, and 2019 respectively. Although most fermented foods are not known for their area of origin, the microbial groups involved in their processing come from the bacterial group rather than fungi, mainly through the lactic acid fermentation mechanism. Microbes' role in fermented products is diverse and can be grouped into five groups. The primary role of microbes is to support bioprocesses. Among milk-based fermented products, dangke is one of the traditional products with a fat content that is significantly different fat content from yogurt, kefir, and dadih, and the protein is not significantly different from yogurt, kefir, dadih, and mozzarella cheese. This nutritional content analysis indicates differences in fat and protein content among fermented milk-based food products. Keywords: dangke, fat content, metadata, protein content, proximate analysis
Co-Authors A M Sabbah, Sajida Agung Priyanto, Jepri Ai Hertati, Ai Akmaliyah, Rizna Alfaridza, Annisa Nourma ALFIYAN, ACHMAD Amani, Febriyanti Nur Anja Meryandini Antonius Suwanto Apon Zaenal Mustopa Aris Tri Wahyudi Armanisa, Khafifah Chairunnisa, Sheila Chihombori, Tatenda Calvin DAROJATUL ULYA Dina Aribah DINI NURDIANI Ekawati, Nurlaili Fathiah, Muhammad Fadhil Fatimah Firyal Noviatanti Nabilah Hartono, Faisal Diniamal Iman Rusmana Irawan, Herman Irmanida Batubara Jendri Mamangkey Jun Nomura Lenka, Audria Bayu Lisdar Idwan Sudirman Mahsunah, Anis Herliyati Manguntungi, Baso Monica Ina Martha Muhammad Zulfiqri, Aldy Mutiara, Ilma Nabila Tsoerayya Gustia Pudjas Nadila Fany Ashafani NISA RACHMANIA MUBARIK Nurfadhilla Rahmadhani Nurhakiki Prastya, Muhammad Eka Puspitasari, Dian Japany Puspitasari, Esti Rahayu Wulan Rakhman, Ira Meylan Nafarah Refli, Redoyan Rifqiyah Nur Umami, Rifqiyah Nur RIKA RAFFIUDIN Ririn Herni Putri Rustam, Yepy Hardi Salsabilah, Nadiyah Sarah Asih Faulina Sarah Asih Faulina, Sarah Asih Satya, Andreas Adhi Sidiq, Muhammad Raffel Sri Budiarti Sri Budiarti Poerwanto Sri Estuningsih Sri Listiyowati Trinugroho, Joko P Uci Cahlia Wulan Tri Wahyuni Yaya Rukayadi Yohanes Bernadino Putera Saju Zulhaerati Zulhaerati