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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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Profile of Gut Bacteria in Hypertensive Patients Based on Terminal Restriction Fragment Length Polymorphism Analysis Ririn Herni Putri; Rika Indri Astuti; Sri Budiarti
HAYATI Journal of Biosciences Vol. 30 No. 3 (2023): May 2023
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.30.3.500-509

Abstract

Hypertension is a severe public health problem due to its high prevalence worldwide. About 7.5 million deaths or 12.8% of all annual deaths worldwide occur due to high blood pressure. The hypertensive disease is also associated with the intestinal bacteria. To our knowledge, the diversity of the gut bacteria in hypertensive patients has not been reported yet in Indonesia. Thus, the aims of this study were to analyze profile of gut bacteria in hypertensive patients compared to non-hypertensive based on metagenomic analysis, Terminal Restriction Fragment Length Polymorphism (T-RFLP). The results of the affiliation analysis of the entire Terminal Restriction Fragments (TRF) contained 6 groups of bacteria from 26 TRFs in hypertensive and non-hypertensive respondents. Cutting the 16S rRNA gene with the BslI restriction enzyme successfully detected intestinal bacterial groups, namely Clostridium subcluster XIVa, Prevotella, Clostridium cluster IV, Clostridium cluster XI, Bacteroides and others. In hypertensive patients, a higher relative abundance of bacterial groups showed in Clostridium cluster XI, Clostridium cluster IV and Clostridium subcluster XIVa. The abundance of Bacteroides and Prevotella groups in hypertensive patients were lower than non-hypertensive. The abundance of enterotype I and enterotype II was lower in hypertensive patients than non-hypertensive. Contrarily to that enterotype III cluster. It is worth noting that the F/B ratio was higher in hypertensive patients than that in non-hypertensive. Our data suggest that the gut bacteria profile of hypertensive patients differs to that non-hypertensive.
Quercetin-Containing Extract from Clove Syzygium aromaticum L. Endophytic Bacteria, Fictibacillus phosphorivorans P1U2, Exhibits Antimutagenic Activity in Yeast Saccharomyces cerevisiae Nadila Fany Ashafani; Rika Indri Astuti; Sri Listiyowati; Irmanida Batubara
HAYATI Journal of Biosciences Vol. 30 No. 4 (2023): July 2023
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.30.4.734-742

Abstract

Metabolites from clove (Syzygium aromaticum L.) have been extensively studied for various pharmacological uses, including quercetin. Endophytic bacteria isolated from plant tissues can produce similar secondary metabolites as their host plants. However, little is known about the antioxidant activity of the endophytic bacterial extract from clove leaves. Amongst the potential bacterial groups, the genera of Bacillus have been widely studied as a source of antioxidants. Thus, this study, we examined the potential antioxidant properties of Bacillus sp., isolated from clove leaves. We have successfully isolated ten endophytic bacteria, of which only one isolate (P1U2) was found non-pathogenic based on a hemolytic assay. Based on the 16S rRNA sequence, P1U2 shared the highest similarity to Fictibacillus phosphorivorans. The extract of extracellular metabolites of P1U2 contains quercetin compounds, based on LC-MS analysis. The results of the antioxidant activity test using the DPPH assay showed that the P1U2 extract had an IC50 value of 161 mg/ml. The supplementation of the extract on culture media reduced the ability of S. cerevisiae to decolorize mutagen malachite green and increased cell viability. Furthermore, the addition of 161 ppm extract was able to counteract UV mutagens effects of UV exposure and toxicity of malachite green, significantly increasing the growth of S. cerevisiae. Suggesting the bioactivity of the extract in combating mutagens. To the best of our knowledge, this is the first study to report a quercetin-rich extract derived from endophytic bacteria, F. phosphorivorans. Thus, further study is required to optimize the synthesis of quercetin from isolate P1U2.
Enhanced Ethanol Production by High Temperature-Tolerance Mutant Pichia kudriavzevii T-T2 in various Carbon and Nitrogen Sources Monica Ina Martha; Rika Indri Astuti; Wulan Tri Wahyuni
Microbiology Indonesia Vol. 14 No. 2 (2020): June 2020
Publisher : Indonesian Society for microbiology

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (532.767 KB) | DOI: 10.5454/mi.14.2.3

Abstract

Previously, we had constructed proline accumulating Pichia kudriavzevii yeast mutant (T-T2) that exhibited high temperature tolerance phenotype. In this study we then analyzed the ethanol production of the particular mutant isolate in various carbon (C) and nitrogen sources (N). Fermentation rate of T-T2 either in 4% glucose or substrate mixture (SM = 2%glucose : 2% xylose) was higher than WT strain. The highest CO2 evolving rate by T-T2 in glucose and SM was 57.0 ml/hour and 51.4 ml/hour, respectively, suggesting that T-T2 was capable of using xylose as C-source. T-T2 resulted significant increase of total evolved CO2 than WT strain in glucose as substrate. T-T2 isolate was capable of producing higher ethanol than its WT strains in various C-sources, including glucose, maltose, sucrose, xylose and SM. However, glucose was found as the most preferable C-source to produce ethanol (3.2%) whereas maltose was the least preferable one. T-T2 was found capable in using inorganic sources (NaNO3) to produce ethanol (2.4%) as compared to other N-sources (urea, (NH4)2SO4, NH4Cl). Ethanol production by T-T2 strain in NaNO3 was 16% higher than its WT strain. This data indicate, that NaNO3 is potentially applied as N source alternative to produce ethanol. Based on our study, mutant strain T-T2 shows higher fermentation rate than its WT strain in various sugar and N-sources. The fact that T-T2 could produce ethanol from SM in a similar fermentation rate to single glucose as substrate, suggesting its potential application in the 2nd generation of bioethanol productions.
The ethanol Production Activity of Indigenous Thermotolerant Yeast Pichia kudriavzevii 1P4 DAROJATUL ULYA; RIKA INDRI ASTUTI; ANJA MERYANDINI
Microbiology Indonesia Vol. 14 No. 4 (2020): December 2020
Publisher : Indonesian Society for microbiology

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (1227.645 KB) | DOI: 10.5454/mi.14.4.1

Abstract

Pichia kudriavzevii 1P4 is a thermotolerant-ethanologenic yeast potential for application in ethanol industry. In this study we evaluated the stress tolerance phenotype of P. kudriavzevii 1P4 in dealing with fermentation related-stresses, including high temperature stress, high sugar content, ethanol content and the fermentation capacity of the particular isolate. Based on spot assay, 1P4 showed stress tolerance phenotype against high sugar concentration for up to 30% sugar content and 10% ethanol stress. In addition, 1P4 was capable to show temperature-stress tolerance phenotype for up to 42oC, suggesting that 1P4 belong to thermotolerant yeast isolate. Fermentative activity was measured by using glucose consumption and ethanol production assay. We evaluated the fermentative and growth rate of 1P4 at various temperature condition which were 27oC, 37oC and 42oC using YPD media (at initial glucose of 2%, 10% and 20%). Interestingly, 1P4 consumed the highest glucose in 20% of concentration at 37oC (15.29%), simultaneously with the highest concentration of ethanol (32.05 g/L ethanol and 0.67 g/L/h ethanol productivity). Cell growth analysis showed that growth of 1P4 isolate increased with higher initial glucose condition yet decreased as temperature during fermentation was raised. The growth rate of 1P4 was found high in 20% initial glucose at 37oC than 2% and 10% at same temperature. In addition, 1P4 exhibited short lag phase at high-temperature fermentation. Our data indicate that 1P4 can potentially be applied as fermentation agent especially in high-temperature ethanol fermentation. Key words: bioethanol production, fermentation related-stress, thermotolerant yeast
Antioxidant Properties of Active Fraction Extract Derived from Yellow-Red Pigment Produced by the Marine Sponge-Associated Bacterium Bacillus haikouensis AGS112 and Identification of Related Compounds Uci Cahlia; Rika Indri Astuti; Jun Nomura; Aris Tri Wahyudi
HAYATI Journal of Biosciences Vol. 30 No. 5 (2023): September 2023
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.30.5.874-884

Abstract

Sponge-associated bacteria can produce bioactive compounds similar to the host. Here, the investigation of antioxidant properties of the yellow-red pigment produced by sponge-associated bacterium AGS112 was conducted using in vitro and in vivo analysis. The 16S rRNA gene sequence showed the sponge-associated bacterium AGS112 has the closest similarity with Bacillus haikouensis C-89 (99%). The crude pigment extract produced by Bacillus haikouensis AGS112 contained both phenolic and flavonoid. The peaks occurred at 412 nm and 664 nm, which indicated as the presence of carotenoids and flavonoids, respectively. The active fraction extract obtained through bio-autography TLC, and had more potent antioxidant activity against DPPH (2,2-diphenyl-1-picrylhydrazyl) compared to the crude pigment extract with an IC50 value of 68.62±0.59 µg/ml and 198.88±1.66 µg/ml, respectively. Moreover, the active fraction extract at the concentration of 35 µg/ml could better enhance the viability of Schizosaccharomyces pombe and achieve the highest expression of sod1 and ctt1 genes. Metabolite profiling using LC-MS analysis confirmed the active fraction extract contains eudesmin and artelastin that might be contributed as antioxidants. These results suggest that the active fraction extract of the yellow-red pigment produced by B. haikouensis AGS112 had potency to be used as candidate for natural antioxidants.
Bioethanol Production from Non-Conventional Yeasts Wickerhamomyces anomalus (Pichia anomala) and Detection of ADH1 Gene Fathiah, Muhammad Fadhil; Hartono, Faisal Diniamal; Astuti, Rika Indri; Listiyowati, Sri; Meryandini, Anja
HAYATI Journal of Biosciences Vol. 31 No. 2 (2024): March 2024
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.31.2.221-228

Abstract

Bioethanol is an organic compound resulted from the fermentation of sugar substrates by microorganisms which is used as alternative energy sources. During bioethanol fermentation yeast are exposed to various fermentation stresses, including temperature, osmotic, and oxidative stresess. Such conditions may decrease ethanol production. We previously isolated fermentation-stress tolerance yeast isolates from traditional Balinese beverages, identified as Wickerhamomyces anomalus BT2, BT5, and BT6. However no data available regarding the bioethanol production of those isolates. Our study indicates that these strains could utilize various sugar substrates (glucose, xylose, maltose, sucrose) in oxidative fermentative media. The highest value of substrate utilization efficiency following 48 hours fermentation was shown by BT6 on glucose (61.02%), BT 2 on xylose (55.44%) and maltose (60.90%). Measurement of ethanol production by Gas Chromatography showed that the strains were able to produce higher ethanol on the glucose substrate than other substrates. For instance, BT6 could produce the highest ethanol production (5.00 g/L) amongst strains tested by using glucose as substrate. Yet, the particular strains could only produce 0.30 g/L and 0.65 g/L by using xylose and maltose, respectively. For further genetic engineering purposes, we detected ADH1 gene from all three isolates, with high homology to the alcohol dehydrogenase from Saccharomyces cerevisiae, Geobacillus stearothermophilus and Pseudomonas aeruginosa. Further strain development can be carried out targeting the ADH1 gene, important for ethanol fermentation.
Aktivitas Antimikrob Minyak Atsiri dan Potensinya sebagai Antiseptik : Antimicrobial Activities of Essential Oils and Their Potential as Antiseptics Rakhman, Ira Meylan Nafarah; Agung Priyanto, Jepri; Astuti, Rika Indri
Jurnal Sumberdaya Hayati Vol. 10 No. 2 (2024): 2024
Publisher : Departemen Biologi, Institut Pertanian Bogor

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.29244/jsdh.10.2.41-47

Abstract

Pathogenic bacterial infection is one of the leading causes of mortality worldwide. Essential oil-based antiseptic is needed to prevent pathogenic infection. This study aimed to analyze the antimicrobial activity of essential oils and their antiseptic potential. The essential oils used were clove oil, patchouli oil, citronella oil, ginger oil, and nutmeg oil. These oils had various antibacterial activities with inhibition zones ranging from 0.3-1.2 cm against Escherichia coli [ATCC 8739], Pseudomonas aeruginosa [ATCC 15442], and Staphylococcus aureus [ATCC 6538], as tested by agar diffusion method. Nutmeg oil had the largest inhibition zone against of three targeted bacteria. Supporting this result, cell viability test showed nutmeg oil in concentration of 500 ppm and 1,000 ppm could inhibit the growth S. aureus up to 62% and 100%, respectively. Analysis of standardized antiseptic based on SNI: EN 1040:2005 proved that nutmeg oil can be used as antiseptic candidate because it was able to reduce the S. aureus more than 5log10 after contact for 1 minute. Our data indicate nutmeg oil can potentially to be applied as an antimicrobial agent and an ingredient of antiseptic products.
Potential Probiotic Yeasts of the Pichia Genus Isolated from ‘Dadih’, a Traditional Fermented Food of West Sumatra, Indonesia Chihombori, Tatenda Calvin; Mustopa, Apon Zaenal; Astuti, Rika Indri; Mutiara, Ilma; Refli, Redoyan; Umami, Rifqiyah Nur; Fatimah; Irawan, Herman; Ekawati, Nurlaili; Trinugroho, Joko P; Akmaliyah, Rizna; Chairunnisa, Sheila; Amani, Febriyanti Nur; Manguntungi, Baso; Hertati, Ai; Mamangkey, Jendri
HAYATI Journal of Biosciences Vol. 32 No. 2 (2025): March 2025
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.32.2.320-340

Abstract

Fermented buffalo milk, known as dadih, serves as a reservoir of potential probiotic yeasts. Over the past two decades, probiotic yeasts have gained increasing attention in both basic and clinical sciences due to their health benefits. This study aimed to isolate and characterize probiotic yeasts from dadih. Yeasts were isolated using yeast Extract, peptone, and dextrose (YPD) medium, and molecularly identified through 18S-rRNA sequencing. Probiotic potential was assessed by evaluating resistance to acidic pH, bile salts, proteolytic, lipolytic, and hemolytic activities. Secondary metabolites produced during fermentation were tested for antimicrobial properties. GBT30 and GBT37 isolates were selected based on their superior performance in probiotic property assays for further analysis. Molecular identification revealed these isolates as Pichia occidentalis (GBT30) and Pichia kudriavzevii (GBT37). Both strains demonstrated in vitro survivability under simulated gastrointestinal conditions and exhibited antimicrobial activity. Whole-genome sequencing of P. kudriavzevii GBT37 identified a genome size of 10,906,850 base pairs, distributed across four chromosomes with a GC content of 38.26%. Notably, secondary metabolite biosynthesis genes were located on contig 7. In addition, 26 probiotic-related genes, including GSY1, HSC82, HSP104, TPS1, ARN1, FLO1, ALA1, SIR2, and others, were identified in P. kudriavzevii GBT37, indicating its potential as a probiotic yeast. The traditional fermentation process of dadih offers probiotic yeasts with promising health benefits, supporting its potential as a functional food.
Effect of Multiple Gene Copy Number of Bacterial Lipase to Increase Lipase Production in Pichia pastoris Puspitasari, Esti; Rustam, Yepy Hardi; Satya, Andreas Adhi; Suwanto, Antonius; Wahyudi, Aris Tri; Astuti, Rika Indri
HAYATI Journal of Biosciences Vol. 32 No. 2 (2025): March 2025
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.32.2.310-319

Abstract

Bacterial lipase poses potential challenges when expressed in eukaryotic protein expression systems such as Pichia pastoris. This research aims to increase extracellular T1.2RQ lipase secretion (free lipase) with multiple gene copy number strategies in Pichia pastoris and it was first performed on lipase from Geobacillus stearothermophilus T1.2. In this study, the T1.2RQ lipase gene from Geobacillus stearothermophilus T1.2 was expressed in Pichia pastoris GS115 through a strategy involving multiple copies of lipase, resulting in increased lipase activity. Three copies of the lipase gene in pPIC9K_T1.2RQ(3x) recombinant plasmid were integrated into the genome of Pichia pastoris GS115, and quantitative analysis using qPCR technique confirmed that the GS115 transformant strain contained six copies of T1.2RQ gene, indicating two integration events. Lipase activity measurement showed that the GS115/T1.2RQ(6x) strain exhibited a 111% increase compared to that containing a copy of the T1.2RQ gene. SDS-PAGE and Zymogram results showed a protein band with a size of 43kDa. Qualitative analysis in LA+TBN media of all strains containing the T1.2RQ gene showed clear zones. Lipase production in flask fermentation took at least 120 hours to produce the best lipase activity. Thus, strategies with multiple copy numbers of gene lipase have significantly increased the expression of the bacterial lipase gene in Pichia pastoris GS115.
Diversity of Rhizospheric Bacterial Community from Kaolin Mining Site and Their Potential as Plant Growth Promoting Bacteria Armanisa, Khafifah; Rusmana, Iman; Astuti, Rika Indri
HAYATI Journal of Biosciences Vol. 32 No. 1 (2025): January 2025
Publisher : Bogor Agricultural University, Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.4308/hjb.32.1.212-222

Abstract

Tailing from mining activities affects soil fertility resulting in poor soil conditions that are challenging for plants to grow. Plants can interact with rhizosphere bacteria to enhance their growth in harsh environments. Rhizospheric bacteria possess numerous mechanisms that promote plant growth and induced resistance to various abiotic stress. This study aims to determine the diversity of rhizobacteria and their potential as plant growth-promoting rhizobacteria (PGPR) agents. Bacterial communities from rhizosphere soil samples from kaolin mining sites in Perawas, Tanjung Pandan district, Belitung Regency, Bangka Belitung Island, Indonesia were analyzed using Next Generation Sequencing based on the V3-V4 region of the 16S rRNA gene, while culturable bacteria were isolated from samples and screened for PGP activity. The results showed that the rhizosphere bacterial community was mostly dominated by Pseudomonadota, Acidobacteria, and Verrumicrobiota. There were 15 bacteria isolated from the sample and RKB-5 bacterial isolate had the potential to be PGP agent. The RKB-5 bacterial isolate was identified as Burkholderia cenocepacia based on its 16S rRNA sequence. The bacterial isolate produced IAA, utilized ACC, dissolved phosphate up to 209,5 mg/L, and formed a high potassium solubilizer index value of 5.00. Therefore, the B. cenocepacia RKB-5 has potential application as the PGPR to support plants growth by obtaining nutrients in ex-mining lands with poor soil conditions.
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