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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

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Professor Wilhelm H. Holzapfel, School of Life Sciences, Handong Global University, Pohang, South Korea. Wilhelm Holzapfel is author or co-author of more than 300 scientific papers, more than 60 book chapters, and edited 5 books. He held former and recent academic positions (Professor, Hon. Professor and Extraordinary
Professor) in Microbiology at various universities, and (until 2007) was Head (Director and Professor) of the Institute of Hygiene and Toxicology in Karlsruhe/Germany. Since 1996 he has been President of the ICFMH of the IUMS.

Dr Brian J.B. Wood, formerly Reader in Applied Microbiology, Strathclyde University, Glasgow, UK. Dr Wood has published numerous papers on food fermentations and related topics in which these organisms participate. He has edited six multi-author books, including The Microbiology of Fermented Foods and titles covering LAB in various connections, and he has also supplied chapters and encyclopedia entries for numerous other publications.

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 Gálvez 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 Švec and Charles M.A.P. Franz

15 The genus Enterococcus 175
Pavel Švec 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 Justè, 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,

Jørgen 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
Jørgen 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 Gálvez 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 Björkroth 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 Björkroth, 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 Björkroth, 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 Gálvez

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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Lactic Acid Bacteria Biodiversity and Taxonomy

Lactic Acid Bacteria Biodiversity and Taxonomy

1444333836

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