Lactic acid bacteria : biodiversity and taxonomy

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Lactic acid bacteria : biodiversity and taxonomy

edited by Wilhelm H. Holzapfel, Brian J.B. Wood,

Wiley Blackwell, 2014

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"This book provides a much-needed and comprehensive account of the current knowledge of the lactic acid bacteria, covering the taxonomy, biochemistry, physiology and molecular biology of these scientifically and commercially important micro-organisms"-- Provided by publisher

"The lactic acid bacteria (LAB) are a group of related micro-organisms that are enormously important in the food and beverage industries, preventing food spoilage and extending shelf life. This is the first reference that provides a much-needed and comprehensive account of the current knowledge of LAB, detailing the taxonomy, biochemistry, physiology, and molecular biology of these scientifically and commercially important micro-organisms. With chapter coverage of every recognized genus and species, this book will enable researchers to fully exploit the industrial, nutritional, and medical applications of these organisms"-- Provided by publisher

Includes bibliographical references and index

収録内容

  • Section I. Introduction: The Lactic Acid Bacteria in present day context
  • Introduction to the LAB
  • Physiology of the LAB
  • Phylogenetics and Systematics
  • Overview on the ecology and biodiversity of the lactic acid bacteria
  • Comparative genomics of Lactobacillus and other lactic acid bacteria
  • Section II. Family Aerococcaceae
  • The genus Abiotrophia
  • Aerococcus
  • The genus Facklamia
  • Minor genera of the Aerococcaceae (Dolosicoccus, Eremococcus, Globicatella, Ignavigranum)
  • Section III. Family Carnobacteriaceae
  • The genus Carnobacterium
  • The Genus Marinilactibacillus
  • The genus Trichococcus
  • The genus Alkalibacterium
  • Minor Genera of Carnobacteriaceae : Allofustis, Alloiococcus, Atopobacter, Atopococcus, Atopostipes, Bavariicoccus, Desemzia, Dolosigranulum, Granulicatella, Isobaculum and Lacticigenium
  • Section IV: The family Enterococcaceae
  • Genus Enterococcus
  • Genus Tetragenococcus
  • Genus Vagococcus
  • Minor genera in Enterococcaceae : Catellicoccus, Melissococcus and Pilibacter
  • Section V. Family Lactobacillaceae
  • The genus Lactobacillus
  • The genus Paralactobacillus
  • The genus Pediococcus
  • The genus Fructobacillus
  • Section V. Family Leuconostocaceae
  • The genus Leuconostoc
  • The genus Oenococcus
  • The genus Weissella
  • Section VII. The family Streptococcaceae
  • Genus Lactococcus
  • Genus Lactovum
  • The genus Streptococcus
  • Section VIII. Physiologically "related" Genera
  • Genus Bifidobacterium with notes on the genera Scardovia and Parascardovia
  • Genus Sporolactobacillus
  • Genera Bacillus, Geobacillus, and Halobacillus
  • The Genera Halolactibacillus and Paraliobacillus

内容説明・目次

内容説明

Lactic Acid Bacteria Biodiversity and Taxonomy Lactic Acid Bacteria Biodiversity and Taxonomy Edited by Wilhelm H. Holzapfel and Brian J.B. Wood The lactic acid bacteria (LAB) are a group of related microorganisms that are enormously important in the food and beverage industries. Generally regarded as safe for human consumption (and, in the case of probiotics, positively beneficial to human health), the LAB have been used for centuries, and continue to be used worldwide on an industrial scale, in food fermentation processes, including yoghurt, cheeses, fermented meats and vegetables, where they ferment carbohydrates in the foods, producing lactic acid and creating an environment unsuitable for the survival of food spoilage organisms and pathogens. The shelf life of the product is thereby extended, but of course these foods are also enjoyed around the world for their organoleptic qualities. They are also important to the brewing and winemaking industries, where they are often undesirable intruders but can in specific cases have desirable benefits. The LAB are also used in producing silage and other agricultural animal feeds. Clinically, they can improve the digestive health of young animals, and also have human medical applications. This book provides a much-needed and comprehensive account of the current knowledge of the LAB, covering the taxonomy and relevant biochemistry, physiology and molecular biology of these scientifically and commercially important microorganisms. It is directed to bringing together the current understanding concerning the organisms' remarkable diversity within a seemingly rather constrained compass. The genera now identified as proper members of the LAB are treated in dedicated chapters, and the species properly recognized as members of each genus are listed with detailed descriptions of their principal characteristics. Each genus and species is described using a standardized format, and the relative importance of each species in food, agricultural and medical applications is assessed. In addition, certain other bacterial groups (such as Bifidobacterium) often associated with the LAB are given in-depth coverage. The book will also contribute to a better understanding and appreciation of the role of LA B in the various ecosystems and ecological niches that they occupy. In summary, this volume gathers together information designed to enable the organisms' fullest industrial, nutritional and medical applications. Lactic Acid Bacteria: Biodiversity and Taxonomy is an essential reference for research scientists, biochemists and microbiologists working in the food and fermentation industries and in research institutions. Advanced students of food science and technology will also find it an indispensable guide to the subject. Also available from Wiley Blackwell The Chemistry of Food Jan Velisek ISBN 978-1-118-38384-1 Progress in Food Preservation Edited by Rajeev Bhat, Abd Karim Alias and Gopinadham Paliyath ISBN 978-0-470-65585-6

目次

List of contributors xiii Acknowledgements xv List of abbreviations xvi Abbreviations for genera and note on pronunciations xix 1 Introduction to the LAB 1 Wilhelm H. Holzapfel and Brian J.B. Wood 1.1 The scope 1 1.2 A little history 7 1.3 Where are the boundaries? 9 2 Physiology of the LAB 13 Akihito Endo and Leon M.T. Dicks 2.1 Metabolism 13 2.2 Energy transduction and solute transport 20 3 Phylogenetics and systematics 31 Peter Vandamme, Katrien De Bruyne and Bruno Pot 3.1 Introduction 31 3.2 Phylogeny and polyphasic taxonomy of LAB 34 3.3 Conclusions and perspectives 39 4 Overview of the ecology and biodiversity of the LAB 45 Giorgio Giraffa 4.1 Introduction 45 4.2 LAB ecology, diversity and metabolism 45 4.3 Importance of LAB in food and feed ecology and biotechnology 46 4.4 LAB as functional cultures 48 4.5 LAB with health-promoting properties 50 4.6 Concluding remarks 51 5 Comparative genomics of Lactobacillus and other LAB 55 Trudy M. Wassenaar and Oksana Lukjancenko 5.1 Introduction 55 5.2 Selection of LAB genomes for comparative analysis 57 5.3 Numerical comparisons of the selected genomes 58 5.4 Phylogeny of the 16S rRNA gene extracted from the genomes 63 5.5 Pan-genome and core genome of protein genes 63 5.6 Comparison of gene function categories 66 5.7 Conclusions 68 Section I The family Aerococcaceae 71 Paul A. Lawson 6 The genus Abiotrophia 75 Paul A. Lawson 6.1 Introduction and historical background 75 6.2 Description of the genus Abiotrophia 76 6.3 Differentiation of Abiotrophia species from other genera 76 6.4 Isolation, cultivation, ecology and medical importance 76 6.5 Species descriptions 78 7 The genus Aerococcus 81 Paul A. Lawson 7.1 Introduction and historical background 81 7.2 Description of the genus Aerococccus 81 7.3 Differentiation of Aerococcus species from other genera 82 7.4 Differentiation of species of the genus Aerococcus from one another 83 7.5 Isolation, cultivation, ecology and medical importance 84 7.6 Species descriptions 86 8 The genus Facklamia 91 Lesley Hoyles 8.1 Introduction 91 8.2 Differentiation of Facklamia species from other genera 91 8.3 Ecological, medical and industrial relevance of Facklamia species 92 8.4 Antimicrobial susceptibilities of members of the genus Facklamia 94 8.5 Differentiation between species of the genus Facklamia 95 8.6 Descriptions of the genus Facklamia and its species 95 9 Minor genera of the Aerococcaceae (Dolosicoccus, Eremococcus, Globicatella, Ignavigranum) 99 Melanie Huch, Cho Gyu-Sung, Antonio Galvez and Charles M.A.P. Franz 9.1 Historical background 99 9.2 Phenotypic differentiation of the minor genera of the Aerococcaceae from other genera 100 9.3 Genotypic delineation of the minor genera of the Aerococcaceae 101 9.4 Isolation, cultivation, ecology and medical importance 102 9.5 Description of the minor genera of the Aerococcaceae and list of species 102 Section II The family Carnobacteriaceae 107 Elena V. Pikuta 10 The genus Carnobacterium 109 Elena V. Pikuta and Richard B. Hoover 10.1 Historical background and chronology of nomenclature 109 10.2 Definition of the genus Carnobacterium 110 10.3 Relationship to other groups 111 10.4 Future perspectives for characterization 112 10.5 Techniques and growth requirements for cultivation 112 10.6 Biodiversity 112 10.7 Importance of the genus and particular species 113 10.8 Other applications and future perspectives 115 10.9 Description of species 115 11 The genus Marinilactibacillus 125 Morio Ishikawa and Kazuhide Yamasato 11.1 Introduction 125 11.2 General and taxonomic characters 125 11.3 Phylogenetic affiliation of Marinilactibacillus species 126 11.4 Physiological properties 127 11.5 Differentiation of Marinilactibacillus from other related species 127 11.6 Lactic acid fermentation and aerobic metabolism of glucose 127 11.7 Ecology and isolation methods 129 11.8 Description of the species of the genus Marinilactibacillus 132 12 The genus Trichococcus 135 Elena V. Pikuta and Richard B. Hoover 12.1 Historical background and chronology of nomenclature for the Trichococcus species 135 12.2 Definition of the genus Trichococcus 136 12.3 Relationship to other genera within the Carnobacteriaceae and other LAB families 136 12.4 Future taxonomic perspectives 139 12.5 Techniques and growth requirements for cultivation of Trichococcus species 139 12.6 Biodiversity 139 12.7 Importance of the genus and particular species 140 12.8 Species descriptions 141 13 The genus Alkalibacterium 147 Isao Yumoto, Kikue Hirota and Kenji Nakajima 13.1 Introduction 147 13.2 Taxonomy 148 13.3 Description of the genus 148 13.4 Enrichment and isolation procedures 148 13.5 Natural habitats 149 13.6 Acid production 150 13.7 Identification of Alkalibacterium species 150 13.8 Overview of the current situation for this genus 150 13.9 Description of species 153 13.10 Concluding remarks 156 14 Minor genera of the Carnobacteriaceae: Allofustis, Alloiococcus, Atopobacter, Atopococcus, Atopostipes, Bavariicoccus, Desemzia, Dolosigranulum, Granulicatella, Isobaculum and Lacticigenium 159 Ulrich Schillinger and Akihito Endo 14.1 Introduction 159 14.2 Taxonomy 159 14.3 Biodiversity of each genus 162 14.4 Practical importance 163 14.5 Species descriptions 164 Section III The family Enterococcaceae 171 Pavel Svec and Charles M.A.P. Franz 15 The genus Enterococcus 175 Pavel Svec and Charles M.A.P. Franz 15.1 Historical background and chronology of nomenclature 175 15.2 Phenotypic differentiation of the genus Enterococcus 178 15.3 Genotypic delineation of the genus Enterococcus 178 15.4 Phylogenetic structure within the genus Enterococcus 179 15.5 Isolation and cultivation 179 15.6 Identification of Enterococcus spp. 179 15.7 Importance of the genus and particular species 182 15.8 Species of the genus Enterococcus 186 16 The genus Tetragenococcus 213 Annelies Juste, Bart Lievens, Hans Rediers and Kris A. Willems 16.1 Introduction 213 16.2 Phenotypic characteristics of the genus Tetragenococcus 215 16.3 Genotypic characteristics of the genus Tetragenococcus 217 16.4 Industrial relevance of the genus Tetragenococcus 221 16.5 Description of species 222 17 The genus Vagococcus 229 Paul A. Lawson 17.1 Introduction and historical background 229 17.2 Description of the genus Vagococcus 229 17.3 Differentiation of Vagococcus species from other genera 230 17.4 Differentiation of species of the genus Vagococcus from one another 231 17.5 Isolation, cultivation, ecology and medical importance 231 17.6 Species descriptions 232 18 Minor genera of the Enterococcaceae (Catellicoccus, Melissococcus and Pilibacter) 239 Leon M.T. Dicks, Akihito Endo and Carol A. Van Reenen 18.1 Introduction 239 18.2 Phylogeny 239 18.3 Morphology 240 18.4 Growth characteristics 240 18.5 Practical importance 241 18.6 Description of species 241 Section IV The family Lactobacillaceae 245 Giovanna E. Felis and Bruno Pot 19 The genus Lactobacillus 249 Bruno Pot, Giovanna E. Felis, Katrien De Bruyne, Effie Tsakalidou, Konstantinos Papadimitriou, Jorgen Leisner and Peter Vandamme 19.1 Historical background 249 19.2 Lactobacillus metabolism 250 19.3 The taxonomy of the genus Lactobacillus 282 19.4 The current phylogenetic structure of the genus Lactobacillus 286 19.5 Food and health applications of the genus Lactobacillus 293 19.6 Short descriptions of the validly published species of the genus Lactobacillus 294 19.7 Lactobacillus species awaiting validation pending publication of the manuscript (March 2013) 327 19.8 Lactobacillus species and subspecies that have been renamed after their original description 329 19.9 Lactobacillus species that have never been validly named, but whose names nonetheless appear in the literature, and their current names 335 20 The genus Paralactobacillus 355 Jorgen J. Leisner and Bruno Pot 20.1 Introduction 355 20.2 Defining the genus as phenotype and genotype 355 20.3 Biodiversity within the genus and species based on phenotype 356 20.4 Importance of the genus and particular species 356 20.5 Description of species 357 21 The genus Pediococcus 359 Charles M.A.P. Franz, Akihito Endo, Hikmate Abriouel, Carol A. Van Reenen, Antonio Galvez and Leon M.T. Dicks 21.1 Historical background and chronology of nomenclature 359 21.2 Phenotypic differentiation of the genus Pediococcus 360 21.3 Genotypic delineation of the genus Pediococcus 360 21.4 Phylogenetic structure within the genus Pediococcus 361 21.5 Isolation and cultivation 362 21.6 Identification of Pediococcus spp 362 21.7 Importance of the genus and particular species 365 21.8 Species of the genus Pediococcus 366 Section V The family Leuconostocaceae 377 Akihito Endo, Leon M.T. Dicks, Johanna Bjoerkroth and Wilhelm H. Holzapfel 22 The genus Fructobacillus 381 Akihito Endo and Leon M.T. Dicks 22.1 Introduction 381 22.2 Phylogenetic relationships 381 22.3 Morphology 383 22.4 Biochemical characteristics 383 22.5 Physiological characteristics 386 22.6 Habitat 386 22.7 Species in the genus Fructobacillus 386 23 The genus Leuconostoc 391 Johanna Bjoerkroth, Leon M.T. Dicks, Akihito Endo and Wilhelm H. Holzapfel 23.1 Historical background, chronology of nomenclature and relationship to other LAB 391 23.2 Definition of the genus as phenotype 392 23.3 Biodiversity within the genus based on phenotype 393 23.4 Genomic studies and genotyping of Leuconostoc 393 23.5 Importance of the genus and particular Leuconostoc species 394 23.6 Description of species of the genus Leuconostoc 395 24 The genus Oenococcus 405 Akihito Endo and Leon M.T. Dicks 24.1 Introduction 405 24.2 Phylogeny and evolution 405 24.3 Morphology 406 24.4 Growth characteristics 407 24.5 Intraspecies diversity 409 24.6 Practical importance 410 24.7 Stress response 410 24.8 Description of species in the genus Oenococcus 412 25 The genus Weissella 417 Johanna Bjoerkroth, Leon M.T. Dicks and Akihito Endo 25.1 Historical background, chronology of nomenclature and relationship to other LAB 417 25.2 Defining the genus as phenotype and genotype 417 25.3 Biodiversity within the genus and within particular species based on phenotype 419 25.4 Importance of the genus and particular species 419 25.5 Descriptions of species in the genus Weisella 421 26 The genus Lactococcus 42 Wonyong Kim 26.1 Introduction 429 26.2 Defining the genus as phenotype and genotype 429 26.3 Biodiversity within the genus based on phenotype 433 26.4 Biodiversity within species based on phenotype 434 26.5 Importance of the genus Lactococcus and species 436 26.6 Description of species of the genus Lactococcus 437 Section VI The family Streptococcaceae 445 Maret du Toit, Melanie Huch, Gyu-Sung Cho and Charles M.A.P. Franz 27 The genus Lactovum 447 Harold L. Drake 27.1 Introduction 447 27.2 Phylogeny and taxonomy of Lactovum 447 27.3 Morphology of Lactovum 448 27.4 Soil: the origin of Lactovum 449 27.5 Growth properties and substrate range of Lactovum 449 27.6 Physiology of Lactovum 451 27.7 Genus description 452 27.8 Conclusion 453 28 The genus Streptococcus 457 Maret du Toit, Melanie Huch, Gyu-Sung Cho and Charles M.A.P. Franz 28.1 Historical background and chronology of nomenclature 457 28.2 Phenotypic differentiation of the genus Streptococcus 458 28.3 Genotypic delineation of the genus Streptococcus 458 28.4 Phylogenetic structure within the genus Streptococcus 459 28.5 Isolation and cultivation 465 28.6 Identification of Streptococcus spp. 466 28.7 Importance of the genus and particular species 475 28.8 Species of the genus Streptococcus 476 Section VII Physiologically 'related' genera 507 Wilhelm H. Holzapfel and Brian J.B. Wood 29 The genera Bifidobacterium, Parascardovia and Scardovia 509 Paola Mattarelli and Bruno Biavati 29.1 Historical background 509 29.2 Taxonomy of the bifidobacteria 514 29.3 Ecology 521 29.4 Health benefits 522 29.5 Industrial applications 523 29.6 Other applications 523 29.7 Description of species 524 29.8 Bifidobacterium: concluding remarks 534 29.9 The genera Parascardovia and Scardovia 534 30 The genus Sporolactobacillus 543 Stephanie Doores 30.1 Introduction 543 30.2 Defining the genus as phenotype and genotype 544 30.3 Importance of the genus and particular species 547 30.4 Description of species of the genus Sporolactobacillus 548 31 The genera Bacillus, Geobacillus and Halobacillus 555 Hikmate Abriouel, Nabil Benomar, Melanie Huch, Charles M.A.P. Franz and Antonio Galvez 31.1 Introduction 555 31.2 The genus Bacillus 556 31.3 Related genera in the family Bacillaceae 563 31.4 Food, health and environmental applications 564 31.5 Concluding remarks 565 32 The genera Halolactibacillus and Paraliobacillus 571 Kazuhide Yamasato and Morio Ishikawa 32.1 Introduction 571 32.2 The genus Halolactibacillus 571 32.3 Paraliobacillus ryukyuensis 578 Appendix: Guidelines for characterizing LAB, bifidobacteria and related genera for taxonomic purposes 583 Paola Mattarelli, Bruno Biavati, Walter Hammes and Wilhelm H. Holzapfel A.1 Introduction 583 A.2 Phenotypic criteria 584 A.3 Genotypic criteria 588 A.4 Additional criteria 589 A.5 Concluding remarks 591 Index 593

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