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Polyphasic Taxonomic Studies Od Lactic Acid Bacteria

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Polyphasic Taxonomic Studies Od Lactic Acid Bacteria POLYPHASIC TAXONOMIC STUDIES OF LACTIC ACID BACTERIA ASSOCIATED WITH NON-FERMENTED MEATS Joanna Koort Department of Food and Environmental Hygiene Faculty of Veterinary medicine University of Helsinki Helsinki, Finland POLYPHASIC TAXONOMIC STUDIES OF LACTIC ACID BACTERIA ASSOCIATED WITH NON-FERMENTED MEATS Joanna Koort Academic Dissertation To be presented with thepermission of the Faculty of Veterinary Medicine, University of Helsinki, for public examination in Walter Hall, Agnes Sjöbergin katu 2, Helsinki, n March 31th, 2006 at 12 noon. Supervisor Professor Johanna Björkroth, DVM, PhD University of Helsinki Finland Reviewers Professor Alexander von Holy, PhD University of Witwaterstrand, Johannesburg South Africa and Doctor Ioannis (John) Samelis, PhD National Agricultural Research Foundation Dairy Research Institute Greece Opponent Professor Kielo Haahtela, PhD University of Helsinki Finland ISBN 952-92-0046-3 (paperback) ISBN 952-10-3018-6 (PDF) Yliopistopaino 2006 ACKNOWLEDGEMENTS................................................................................................ 6 ABBREVIATIONS ............................................................................................................ 7 ABSTRACT........................................................................................................................8 LIST OF ORIGINAL PUBLICATIONS.......................................................................... 11 1 INTRODUCTION ........................................................................................................ 12 2 REVIEW OF THE LITERATURE .............................................................................. 14 2.1 LACTIC ACID BACTERIA ............................................................................. 14 2.1.1 LAB in meat and non-fermented meat products....................................... 17 2.2 THE CURRENT BACTERIAL SPECIES CONCEPT..................................... 19 2.3 THE POLYPHASIC APPROACH IN LAB TAXONOMY ............................. 21 2.3.1 The golden triad: DNA-DNA reassociation, G+C% and 16S rRNA encoding gene sequence............................................................................ 22 2.3.2 Sequencing of other housekeeping genes ................................................. 24 2.3.3 16S and 23S rRNA gene RFLP (Ribotyping)........................................... 24 2.3.4 Other DNA profiling methods .................................................................. 25 2.3.5 Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS- PAGE) of whole-cell protein extracts............................................ 26 2.3.6 Cell wall composition ............................................................................... 26 2.3.7 Cellular fatty acids.................................................................................... 27 2.3.8 Classical phenotypic characters: physiological and biochemical characters and morphology....................................................................... 28 2.4 HISTORY OF THE LAB GENERA RELEVANT IN MEAT ECOSYSTEMS.................................................................................................. 29 2.4.1 LAB with coccoid morphology ................................................................ 30 2.4.2 LAB with bacilliform morphology ........................................................... 32 2.4.3 LAB with both cocci and bacilliforms: Weissella .................................... 33 3 AIMS OF THE STUDY ............................................................................................... 34 4 MATERIALS AND METHODS.................................................................................. 35 4.1 BACTERIAL STRAINS AND CULTURING (I-V)......................................... 35 4.2 RIBOTYPING (I-V).......................................................................................... 37 4 4.3 MORPHOLOGY AND PHENOTYPICAL TESTS (I-IV) ............................... 38 4.4 SDS-PAGE OF WHOLE-CELL PROTEIN EXTRACTS ................................ 39 4.5 SEQUENCING OF 16S rRNA ENCODING GENE (I-V) ............................... 39 4.6 DETERMINATION OF THE G+C CONTENT AND DNA-DNA REASSOCIATION LEVELS (I-V)................................................................... 40 5 RESULTS ..................................................................................................................... 41 5.1 LACTOBACILLUS CURVATUS SUBSP. MELIBIOSUS (I)............................. 41 5.2 ENTEROCOCCUS HERMANNIENSIS (II) AND LACTOBACILLUS OLIGOFERMENTANS (III) SP. NOV............................................................... 41 5.3 STREPTOCOCCUS PARAUBERIS (IV) AND WEISSELLA VIRIDESCENS (V) ............................................................................................ 42 6 DISCUSSION............................................................................................................... 43 6.1 LACTOBACILLUS CURVATUS SUBSP. MELIBIOSUS (I)............................. 43 6.2 ENTEROCOCCUS HERMANNIENSIS (II) AND LACTOBACILLUS OLIGOFERMENTANS (III) SP. NOV............................................................... 44 6.3 STREPTOCOCCUS PARAUBERIS (IV) AND WEISSELLA VIRIDESCENS (V) ............................................................................................ 46 6.4 POLYPHASIC APPROACH............................................................................. 47 7 CONCLUSIONS........................................................................................................... 51 5 ACKNOWLEDGEMENTS This study was carried out at the Department of Food and Environmental Hygiene, Faculty of Veterinary Medicine, University of Helsinki, in 2002-2005. The financial support of the Academy of Finland (Biodiversity and taxonomy of psychrotrophic lactic acid bacteria associated with food spoilage, project no. 100479) is gratefully acknowledged. I owe my sincere thanks to all the many people who have been involved and have helped me during this project. In addition, I would like to express special gratitude to: Professor Johanna Björkroth, my supervisor, for her everlasting encouragement and patience. Professor Hannu Korkeala, Head of the Department of Food and Environmental Hygiene, for placing the facilities of the department at my disposal, and for his continuous efforts to develop the scientific level of veterinary food hygiene. All the co-authors, especially Peter Vandamme and Tom Coenye, for all their help as well with the papers as with the other parts of this project. Ms. Henna Niinivirta, for her excellent technical assistance in this project, and also for our friendship. All the other people in the department, especially in the DNA lab, for the pleasant atmosphere. Special thanks for Kirsi Ristkari and Johanna Seppälä for all their help. Docent Anja Siitonen, for awakening my interest in microbes and the world of making research, and all my former colleagues in the Laboratory of Enteric Pathogens, The National Pubic Health Institute. My parents, for their support especially during the very early years in my studies, and my husband, Sami Helin, for his support, encouragement, and especially patience. 6 ABBREVIATIONS AFLP amplified fragment length polymorphism fAFLP fluorescent AFLP CCUG Culture Collection, University of Göteborg, Sweden DAP diaminopimelic acid ddNTP dideoxynucleotide DSM Deutsche Sammlung von Mikroorganismen und Zellkulturen (German Collection of Microorganisms and Cell Cultures) EMP Embden-Meyerhof-Parnas metabolic pathway HPLC high performance liquid chromatography ICSP International Committee on Systematics of Prokaryotes IUMS International Union of Microbiological Societies LAB lactic acid bacteria LMG bacterial culture collection in Laboratorium voor Microbiologie, Gent; a part of BCCMTM, The Belgian Co-ordinated Collections of Micro- organisms MAP modified atmosphere packaging MLST multi locus sequence typing OTU operational taxonomic unit PCR polymerase chain reaction RAPD random amplified polymorphic DNA RFLP restriction fragment length polymorphism SDS- PAGE sodium dodecyl sulfate-polyacrylamide gel electrophoresis SNP single nucleotide polymorphism UPGMA unweighted pair group method with arithmetic averages 7 ABSTRACT To study the taxonomy of L. curvatus subsp. melibiosus and four independent groups of other lactic acid bacterium (LAB) isolates associated with non-fermented meats, a polyphasic taxonomic approach was applied. The methods used included 16S rRNA gene sequence analysis, DNA-DNA reassociation, DNA base ratio determination, numerical analysis of 16 and 23 S rRNA gene RFLP (ribotypes) and whole cell protein patterns, and the examination of some essential phenotypic properties chosen in compliance with the genus. In addition to the studies of the taxonomic position of these meat-associated LAB, the overall performance of the polyphasic approach in the taxonomy of these LAB was evaluated. In several independent studies dealing with Lactobacillus sakei and Lactobacillus curvatus, the subspecies division of L. curvatus, and especially the taxonomic position of L. curvatus subsp. melibiosus has been found to be controversial. Therefore, the T taxonomic position of L. curvatus subsp. melibiosus CCUG 34545 was re-evaluated in a polyphasic taxonomy study. On the basis of the results obtained, it was proposed that the T subspecies division within L. curvatus should be abandoned and the strain CCUG 34545 T and its duplicate CCUG 41580 be reclassified as Lactobacillus sakei subsp.
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