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Analysis of Phylogenetic Lactic Acid Bacteria in Glutinous Rice “Tape Ketan” by Bioinformatic Tools in Relation with Its Bacteriocin Product

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ANALYSIS OF PHYLOGENETIC LACTIC ACID BACTERIA IN GLUTINOUS RICE “TAPE KETAN” BY BIOINFORMATIC TOOLS IN RELATION WITH ITS BACTERIOCIN PRODUCT 1RINI NUR’AZIZAH, 2ISTIQOMAH SARI KUMARAWATI 1,2Faculty of Biology, Gadjah Mada University, Yogyakarta, Indonesia E-mail: [email protected] Abstract— Glutinous rice or Tape Ketan is fermented food in Indonesia with prepared using ketan or Oryza sativa glutinosa using ragi as a starter. Tape ketan consumed for its taste, flavor, nutrients, and easy digestibility, it has a sweet-acid and mild alcoholic flavor. It producing Lactic Acid Bacteria asLactobacillus curvatus, Lactobacillus fermentum, Pediococcus pentosaceous, Enterococcus villorum, Weissella Confusa, Weissella paramesenteroides, Enterococcus faecium and Weissella kimchii. Analysis of philogenetic was done by Bioinformatic tool, it use 16S rRNA gene sequences retrieved from NCBI database with the distance based and character based methods. It was used ClustalX 2.1 for multiple sequences aligenment and Mega 6 software to build phylogenetic tree. Keywords— Lactic Acid Bacteria, Tape ketan, Glutinous rice, Bioinformatic. I. INTRODUCTION represented by treelike diagrams, it is estimated pedigree of the inherited relationships with overall Tape ketan or glotinous rice is popular fermented similirity [12]. Cladistic analysis of morphological food in Indonesia. Tape ketan is prepared using ketan characters and phenetic, cladistic or maximum- or Oryza sativa glutinosa using ragi as a starter. Tape likehood analysis of molecular character are the key ketan has a sweet-acid taste and mild alcoholic flavor. methods for phylogenies [13]. Bioinformatics is It is because fermentation. Fermentation can increase combination science between biology and the taste, nutritional and organoleptic like flavors, information technique or computer science. The dutty aromas and textures [1]. Tape ketan is produced on of bioinformatics is to solve problems molecular home industry in Indonesia with solid-state biology in computing. These problems is not only fermentation in traditional scale[2,3]. Tape ketan also fundamental things as solve of enzyme mechanism, produce Lactic Acid Bacteria (LAB). LAB is group protein metabolism or identification of microbes but of gam positive bacteria, nonsporulating, rods or also biomedical problems, design of medicine, cocci shape, nonaerobic, aerotolerant and producing primary, vaccine can be resolved [14]. Bioinformatics lactic acid as a result of fermentation [4]. LAB is used to phylogenetic analysis also. It use computer produce bacteriocins, bacteriocins are synthesized in software, as Clustal X for multiple sequences ribosome form peptides as antimicrobial those are aligenment and Mega 6 software to build active against othe bacteria, like pathogen microbia phylogenetic tree. Taxonomic studies on LAB from [5].Bacteriocins are divided into several classes. tape ketan are not yet complete.Thus, it is important Group I, also known as lantibiotic. Group II is to classify and identify LAB from tape ketan on the subdivided into three groups : subgroup basis not only of phenotypic characteristics but also IIa,bacteriocins active against Listeria phylogenetic analysis by 16S rRNA sequencing and monocytogenes, and pediocin PA-1,sakacins A and P, bioinformatic tools leucocin A, bavaricin MN and curvacin A are members of this group; then subgroup IIb require two II. MATERIALS AND METHOD different peptides for activity andlactococcins G and M, and lactacin F are members of it; and subgroup Samples were collected by literature searched both IIc, such as lactacin B, group IId such as lacticin. online or offline. Then, 16S rRna sequence were Group III are such as helveticins J andV, and retrieving from NCBI, there are Lactobacillus lactacins A and B. Leuconocin S, lactocin and curvatus(AB025183), Lactobacillus pediocin SJ-1 have lipid or carbohydrate moieties and fermentum(AF477498), Pediococcus are classified into group IV [6, 7]. The LABs pentosaceous(JX141316), Enterococcus produced by tape ketan areLactobacillus curvatus, villorum(AF335596), Weissella Confusa(LC063164), Lactobacillus fermentum, Pediococcus pentosaceous, Weissella paramesenteroides(KM392070), Enterococcus villorum, Weissella Confusa, Weissella Enterococcus faecium (AF039901) and Weissella paramesenteroides, Enterococcus faecium and kimchii(AF312874).In these sequences little changes Weissella kimchii [8, 9, 10, 11]. occurduring evolution. The sequences are colected in Phylogenetic is study of relationship specieses based one notepad. Then, sequences alignment were done on evolution, these relationship is estimated by by ClustalX, the result of allignment is used to the phylogenetic analysis.It generates branching, and next step, build a phylogenetic tree by software Proceedings of 24th ISERD International Conference, Seoul, South Korea, 13th January 2016, ISBN: 978-93-82702-10-8 26 Analysis of Phylogenetic Lactic Acid Bacteria in Glutinous Rice “Tape Ketan” by Bioinformatic Tools in Relation With its Bacteriocin Product MEGA6, insertion and deletion are treated for belong to filum Firmicutes, classes Bacilli, family missing datas, all character have same values and all Lactobacilalles, order Lactobacillaceae (L. curvatus, data is analyzed with kimura 2-parameter model with L. fermentum, P. pentosaceous), Enterococcaceae (E. 1000 bootstrap. villorum, E. faecium) and Leuconostocaceae (W. confusa, W. paramesenteroidesand W. kimchii) [] III. RESULTS AND DISCUSSIONS There are 8 species Lactic Acid Bacteria that found in Tape ketan after the literature survey, those are Table 1. Lactic Acid Bacteria and its Bacteriocins Product Bacteriocins produced Lactic Acid Bacteria, can as fermentumproduce class I bacteriocins, that is probiotics. Bacteria produce this bacteriocins during Fermentacin, it is lantibiotics containing, has nisin as their growth, substances ofprotein structure (either the first and known bacteriocin while L. proteins or polypeptides), possessing antimicrobial curvatusproduce IIa bacteriocins, A circular activities. Nowadays, bacteriocins have been widely bacteriocins [6,7]. L. curvatus, E. fillorum and E. utilised especially in food preservation[15].One of faecium grouping into one clade, genus Enterococcus food that containing LAB and produce bacteriocins is produce enterocins. That is include class IIb tape ketan, a traditional food from Indonesia that bacteriocins, two-peptide bacteriocins[6]. made from glutinous rice with solid stade fermentation method. CONCLUSION Based on the research, can be conclused that tape ketan or glotinous rice is popular fermented food in Indonesia, produce bacteriocins from LAB. Taxonomy of LAB is not only based on phenetic analysis, but also with phylogenetic analysis. Analysis phylogenetic LAB in Tape ketan using bioinformatic tools generates two clades. REFERENCES [1] Nuraida, L. 2015. A review: Health promoting lactic acid bacteria in traditional Indonesian Figure 1. Phylogenetic tree of the LAB was prepared by fermented foods. Food Science and Human Neighbour Joining method (bootstrap analysis) Wellness, 6(1), 1-9. [2] Djien, K. S. 1972. Tape Fermentation. Applied Figure 1 showed that LAB from tape ketan have two Microbiology, 23(5), 976-978. clades, clade one is a group of W. kimchii,W. confusa, [3] Law, S. V., Abu Bakar, F., Mat Hashim, D. And W. paramesenteroides, andL. fermentumwith 100 Abdul Hamid, A. 2011. Mini Review: Popular fermented food and beverages in southeast Asia. values of bootstrap and second clade is group of L. International Food Research Journal, 18, 475-484. curvatus, E. villorum and E. faecium with 100 values [4] Gautam, P., Anjhurda, V. 2014. Phylogenetic of bootstrap. W. kimchiiis closest sequence with W. analysis of selected acid bacteria by using paramesenteroidesand W. confusawith similirity bioinformatic tools. International Journal of Engineering and Technical Research, 2(8), 53-58. 99%, they are one genus, equally produce Class IId [5] Yang, E., Lihua, F., Yueming, J., Craig, D., Sherry, bacteriosins, that is non-lanthionine-containing F. 2012. Antimicrobial activity of bacteriocin- bacteriocins, and unmodified, linear, non-pediocin- producing lactic acid bacteria isolated from cheeses like bacteriocins [7].The research result indicates and yoghurts. AMB Express, 2(48), 1-12. [6] Quinto, E. J., Pilar, J., Irma, C., Jesus, T., Javier, M. thatL. fermentum and L. curvatus which is one genus Tomas, G. 2014. Probiotic lactic acid bacteria: a are in different clade, ir is because of previous studies review. Food and Nutrition Sciences, 5, 1765-1775. have shown that the genus Lactobacillus isa [7] Perez, R. H., Takeshi, Z., Kenji, S. 2014. Novel heterogeneous group with unstable taxonomy [16].L. bacteriocins from lactic acid bacteria (LAB): Proceedings of 24th ISERD International Conference, Seoul, South Korea, 13th January 2016, ISBN: 978-93-82702-10-8 27 Analysis of Phylogenetic Lactic Acid Bacteria in Glutinous Rice “Tape Ketan” by Bioinformatic Tools in Relation With its Bacteriocin Product Various structure and applications. Microbial Cell [12] Baxevanis, A. D., Oullette, B. F. F. 2001. Factories 2014, 13(1), 1-13. Bioinformatics: A practical guide to the analysis of [8] Hadisepoetro, E.S.S., Takada, N. and Oshima, Y. genes and proteins, second edition. John Wiley & 1979.Microflora in ragi and usar. Journal of Sons. London. Pp: 323-325. Fermentation Technology, 57, 251-259. [13] Benton, M. J. 2000. Stems, nodes, crown clades, [9] Hasseltine, C. W., Ray, M. L. 1988.
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    Molecular characterization and population dynamics of lactic acid bacteria during the fermentation of sorghum by EVELYN MADOROBA Submitted in partial fulfilment of the requirements for the degree of Philosophiae Doctor in the Faculty of Natural and Agricultural Sciences University of Pretoria Pretoria March 2009 © University of Pretoria TABLE OF CONTENTS DECLARATION…………….………...………………………………….…….………......iii ACKNOWLEDGEMENTS…………………………………………….……..……………iv DEDICATION………………………………………………………………………………v SUMMARY………………………………………………………………………………….vi LIST OF FIGURES………………………………………………………………………...viii LIST OF TABLES…………………………………………………………………………..ix LIST OF ABBREVIATIONS………………………………………………………………x RESEARCH COMMUNICATIONS……………………………………………………....xii CHAPTER ONE…………………………………………………………………………….1 LITERATURE REVIEW CHAPTER TWO……………………………………………………………………………55 POLYPHASIC TAXONOMIC CHARACTERIZATION OF LACTIC ACID BACTERIA ISOLATED FROM SPONTANEOUS SORGHUM FERMENTATIONS USED TO PRODUCE TING, A TRADITIONAL SOUTH AFRICAN FOOD CHAPTER THREE…………………………………………………………………………70 DIVERSITY AND DYNAMICS OF BACTERIAL POPULATIONS DURING SPONATNEOUS FERMENTATIONS USED TO PRODUCE TING, A SOUTH AFRICAN FOOD CHAPTER FOUR………………………………………………………………………….103 USE OF STARTER CULTURES OF LACTIC ACID BACTERIA IN THE PRODUCTION OF TING, A SOUTH AFRICAN FERMENTED FOOD CHAPTER FIVE………………………………………………………………………..….139 GENERAL DISCUSSION AND CONCLUSIONS APPENDICES……………………………………………………………………………...143 ii DECLARATION I declare that the thesis, which I hereby submit for the degree, Philosophiae Doctor (Microbiology)
  • Redalyc.Effects of Fermentation Substrates and Conservation Methods on the Viability and Antimicrobial Activity of Weissella

    Redalyc.Effects of Fermentation Substrates and Conservation Methods on the Viability and Antimicrobial Activity of Weissella

    Electronic Journal of Biotechnology E-ISSN: 0717-3458 [email protected] Pontificia Universidad Católica de Valparaíso Chile Serna-Cock, Liliana; Enríquez-Valencia, Cruz E.; Jiménez-Obando, Eliana M.; Campos-Gaona, Rómulo Effects of fermentation substrates and conservation methods on the viability and antimicrobial activity of Weissella confusa and its metabolites Electronic Journal of Biotechnology, vol. 15, núm. 3, 2012, pp. 1-8 Pontificia Universidad Católica de Valparaíso Valparaíso, Chile Available in: http://www.redalyc.org/articulo.oa?id=173323432006 How to cite Complete issue Scientific Information System More information about this article Network of Scientific Journals from Latin America, the Caribbean, Spain and Portugal Journal's homepage in redalyc.org Non-profit academic project, developed under the open access initiative Electronic Journal of Biotechnology ISSN: 0717-3458 Electron. J. Biotechnol. http://www.ejbiotechnology.info DOI: 10.2225/vol15-issue3-fulltext-9 RESEARCH ARTICLE Effects of fermentation substrates and conservation methods on the viability and antimicrobial activity of Weissella confusa and its metabolites Liliana Serna-Cock1 · Cruz E. Enríquez-Valencia2 · Eliana M. Jiménez-Obando1 · Rómulo Campos-Gaona2 1 Universidad Nacional de Colombia, Sede Palmira, Facultad de Ingeniería y Administración, Valle, Colombia 2 Universidad Nacional de Colombia, Sede Palmira, Facultad de Ciencias Agropecuarias, Valle, Colombia Corresponding author: [email protected] Received October 9, 2011 / Accepted May 15, 2012 Published
  • Effects of Fermentation Substrates and Conservation Methods on the Viability and Antimicrobial Activity of Weissella Confusa and Its Metabolites

    Effects of Fermentation Substrates and Conservation Methods on the Viability and Antimicrobial Activity of Weissella Confusa and Its Metabolites

    Electronic Journal of Biotechnology ISSN: 0717-3458 Electron. J. Biotechnol. http://www.ejbiotechnology.info DOI: 10.2225/vol15-issue3-fulltext-9 RESEARCH ARTICLE Effects of fermentation substrates and conservation methods on the viability and antimicrobial activity of Weissella confusa and its metabolites Liliana Serna-Cock1 · Cruz E. Enríquez-Valencia2 · Eliana M. Jiménez-Obando1 · Rómulo Campos-Gaona2 1 Universidad Nacional de Colombia, Sede Palmira, Facultad de Ingeniería y Administración, Valle, Colombia 2 Universidad Nacional de Colombia, Sede Palmira, Facultad de Ciencias Agropecuarias, Valle, Colombia Corresponding author: [email protected] Received October 9, 2011 / Accepted May 10, 2012 Published online: May 15, 2012 © 2012 by Pontificia Universidad Católica de Valparaíso, Chile Abstract Lactic acid bacteria produce metabolites with antagonistic activity against other bacteria. However, growth conditions and conservation methods may reduce the viability and antimicrobial activity of lactic acid bacteria. This study evaluated the effects of fermentation substrate, lyophilization (freeze-drying) and refrigeration on the viability and antimicrobial activity of Weissella confusa strain and its metabolites against pathogens responsible for bovine mastitis. W. confusa strain was grown in MRS broth and milk supplemented with yeast extract and glucose (MYEG). The collected fractions were preserved by lyophilization or under refrigeration at 4ºC. Every seven days, the viability of W. confusa strain and the stability of its metabolites were evaluated against Staphylococcus aureus and Streptococcus agalactiae by disc diffusion assays. In both fermentation substrates, the combination of lyophilized strain and metabolites retained antimicrobial activity against the two pathogens for 42 days. Also, W. confusa strain retained adequate viability and antimicrobial activity when grown in MYEG and stored under refrigeration conditions.
  • 16S Rdna Metabarcoding of the Bacterial Community Associated with Workers of Pheidole Rugaticeps Emery (Hymenoptera: Formicidae)

    16S Rdna Metabarcoding of the Bacterial Community Associated with Workers of Pheidole Rugaticeps Emery (Hymenoptera: Formicidae)

    Journal of Asia-Pacific Entomology 24 (2021) 176–183 Contents lists available at ScienceDirect Journal of Asia-Pacific Entomology journal homepage: www.elsevier.com/locate/jape Full length article 16S rDNA metabarcoding of the bacterial community associated with workers of Pheidole rugaticeps Emery (Hymenoptera: Formicidae) Mohammed Ahmed Ashigar a,b, Abdul Hafiz Ab Majid b,* a Department of Zoology, Federal University of Lafia, Nasarawa State, Nigeria, Lafia 950101, Nigeria b Household & Structural Urban Entomology Laboratory, Vector Control Research Unit, School of Biological Sciences, Universiti Sains Malaysia, Penang 11800 Minden, Malaysia ARTICLE INFO ABSTRACT Keywords: Insect microbiota are receiving increasing attention from researchers, particularly with the continued advances Acinetobacter in next generation sequencing (NGS) techniques. However, there is a paucity of data on the microbiota of ants A. baumannii that scavenge around human settlements. In this study, we characterized the bacterial communities of Pheidole Firmicutes rugaticeps Emery that were collected scavenging on other household insects using Illumina MiSeq high- Household ants throughput sequencing of the bacterial 16S ribosomal DNA gene. P. rugaticeps DNA was extracted from the in­ P. rugaticeps ™ ’ Microbiome sect samples using a HiYield Genomic DNA isolation kit according to the manufacturer s protocols and Proteobacteria amplified using polymerase chain reaction (PCR). The PCR products were sequenced with the Illumina MiSeq Scavenging ants platform according to the standard protocols to amplify the V3–V4 of the 16S rDNA gene. The results for the 16S rDNA genes were analysed using QIIME 2 Core 2020.6, and a 16S rDNA metabarcoding dataset was presented. A total of 46,651 reads were obtained from three genomic samples.
  • Evaluation of the Functional Potential of Weissella and Lactobacillus Isolates Obtained From

    Evaluation of the Functional Potential of Weissella and Lactobacillus Isolates Obtained From

    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Digital.CSIC 1 Title: Evaluation of the functional potential of Weissella and Lactobacillus isolates obtained from 2 Nigerian traditional fermented foods and cow´s intestine. 3 4 Authors: Funmilola A. Ayenia,b, Borja Sáncheza, Bolanle A. Adeniyib, Clara G. de los Reyes- 5 Gavilána, Abelardo Margollesa, and Patricia Ruas-Madiedoa,* 6 7 Addresses: 8 a Department of Microbiology and Biochemistry of Dairy Products. Instituto de Productos 9 Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC). 10 Villaviciosa, Asturias, Spain. 11 b Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, 12 Ibadan, Oyo State, Nigeria. 13 14 * Corresponding author: Instituto de Productos Lácteos de Asturias, Consejo Superior de 15 Investigaciones Científicas (IPLA-CSIC). Carretera de Infiesto s/n, 33300 Villaviciosa, Asturias, 16 Spain. 17 Tel.: +34 985892131, Fax: +34 985892233, E-mail: [email protected] 18 1 19 ABSTRACT 20 The characterization of 24 lactic acid bacteria (LAB) isolates from Nigerian traditional 21 fermented dairy foods, including some cow´s intestine isolates, was conducted in order to select 22 isolates for potential use as probiotics. LAB isolates were identified by partial sequencing the 23 16S rRNA gene as belonging to the species Lactobacillus paracasei, Lactobacillus brevis and 24 mainly Weissella confusa. At the end of a characterization process, 2 L. paracasei and 2 W. 25 confusa isolates were selected, and their resistance to a simulated gastrointestinal digestion and 26 their ability to adhere to eukaryotic cell lines was assessed.
  • Microbiology and Fermentation of Fermented Foods.Pdf

    Microbiology and Fermentation of Fermented Foods.Pdf

    Microbiology and Technology of Fermented Foods Robert W. Hutkins Microbiology and Technology of Fermented Foods The IFT Press series reflects the mission of the Institute of Food Technologists—advancing the science and technology of food through the exchange of knowledge. Developed in part- nership with Blackwell Publishing, IFT Press books serve as essential textbooks for academic programs and as leading edge handbooks for industrial application and reference. Crafted through rigorous peer review and meticulous research, IFT Press publications represent the latest, most significant resources available to food scientists and related agriculture profes- sionals worldwide. IFT Book Communications Committee Ruth M. Patrick Dennis R. Heldman Theron W. Downes Joseph H. Hotchkiss Marianne H. Gillette Alina S. Szczesniak Mark Barrett Neil H. Mermelstein Karen Banasiak IFT Press Editorial Advisory Board Malcolm C. Bourne Fergus M. Clydesdale Dietrich Knorr Theodore P. Labuza Thomas J. Montville S. Suzanne Nielsen Martin R. Okos Michael W. Pariza Barbara J. Petersen David S. Reid Sam Saguy Herbert Stone Kenneth R. Swartzel Microbiology and Technology of Fermented Foods Robert W. Hutkins Titles in the IFT Press series • Biofilms in the Food Environment (Hans P. Blaschek, Hua Wang, and Meredith E. Agle) • Food Carbohydrate Chemistry (Ronald E. Wrolstad) • Food Irradiation Research and Technology (Christopher H. Sommers and Xuetong Fan) • High Pressure Processing of Foods (Christopher J. Doona, C. Patrick Dunne, and Florence E. Feeherry) • Hydrocolloids in Food Processing (Thomas R. Laaman) • Multivariate and Probabilistic Analyses of Sensory Science Problems (Jean-Francois Meullenet, Hildegarde Heymann, and Rui Xiong) • Nondestructive Testing of Food Quality (Joseph Irudayaraj and Christoph Reh) • Preharvest and Postharvest Food Safety: Contemporary Issues and Future Directions (Ross C.