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 vec and Charles M.A.P. Franz
15 The genus Enterococcus 175
Pavel vec 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
