Lactic Acid Bacteria

About the Editors Professor Wilhelm H. Holzapfel, School of Life Sciences, Handong Global University, Pohang, Gyeongbuk, South Korea. Wilhelm Holzapfel is author or co-author of more than 300 scientific papers and over 60 book chapters, and has edited five books. He has held academic positions (Professor, Honorary 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 Institute for Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, Scotland, UK. Brian 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 xiiiAcknowledgements xvList of abbreviations xviAbbreviations for genera and note on pronunciations xix1 Introduction to the LAB 1Wilhelm H. Holzapfel and Brian J.B. Wood1.1 The scope 11.2 A little history 71.3 Where are the boundaries? 92 Physiology of the LAB 13Akihito Endo and Leon M.T. Dicks2.1 Metabolism 132.2 Energy transduction and solute transport 203 Phylogenetics and systematics 31Peter Vandamme, Katrien De Bruyne and Bruno Pot3.1 Introduction 313.2 Phylogeny and polyphasic taxonomy of LAB 343.3 Conclusions and perspectives 394 Overview of the ecology and biodiversity of the LAB 45Giorgio Giraffa4.1 Introduction 454.2 LAB ecology, diversity and metabolism 454.3 Importance of LAB in food and feed ecology and biotechnology 464.4 LAB as functional cultures 484.5 LAB with health-promoting properties 504.6 Concluding remarks 515 Comparative genomics of Lactobacillus and other LAB 55Trudy M. Wassenaar and Oksana Lukjancenko5.1 Introduction 555.2 Selection of LAB genomes for comparative analysis 575.3 Numerical comparisons of the selected genomes 585.4 Phylogeny of the 16S rRNA gene extracted from the genomes 635.5 Pan-genome and core genome of protein genes 635.6 Comparison of gene function categories 665.7 Conclusions 68Section I The family Aerococcaceae 71Paul A. Lawson6 The genus Abiotrophia 75Paul A. Lawson6.1 Introduction and historical background 756.2 Description of the genus Abiotrophia 766.3 Differentiation of Abiotrophia species from other genera 766.4 Isolation, cultivation, ecology and medical importance 766.5 Species descriptions 787 The genus Aerococcus 81Paul A. Lawson7.1 Introduction and historical background 817.2 Description of the genus Aerococccus 817.3 Differentiation of Aerococcus species from other genera 827.4 Differentiation of species of the genus Aerococcus from one another 837.5 Isolation, cultivation, ecology and medical importance 847.6 Species descriptions 868 The genus Facklamia 91Lesley Hoyles8.1 Introduction 918.2 Differentiation of Facklamia species from other genera 918.3 Ecological, medical and industrial relevance of Facklamia species 928.4 Antimicrobial susceptibilities of members of the genus Facklamia 948.5 Differentiation between species of the genus Facklamia 958.6 Descriptions of the genus Facklamia and its species 959 Minor genera of the Aerococcaceae (Dolosicoccus, Eremococcus, Globicatella, Ignavigranum) 99Melanie Huch, Cho Gyu-Sung, Antonio Gálvez and Charles M.A.P. Franz9.1 Historical background 999.2 Phenotypic differentiation of the minor genera of the Aerococcaceae from other genera 1009.3 Genotypic delineation of the minor genera of the Aerococcaceae 1019.4 Isolation, cultivation, ecology and medical importance 1029.5 Description of the minor genera of the Aerococcaceae and list of species 102Section II The family Carnobacteriaceae 107Elena V. Pikuta10 The genus Carnobacterium 109Elena V. Pikuta and Richard B. Hoover10.1 Historical background and chronology of nomenclature 10910.2 Definition of the genus Carnobacterium 11010.3 Relationship to other groups 11110.4 Future perspectives for characterization 11210.5 Techniques and growth requirements for cultivation 11210.6 Biodiversity 11210.7 Importance of the genus and particular species 11310.8 Other applications and future perspectives 11510.9 Description of species 11511 The genus Marinilactibacillus 125Morio Ishikawa and Kazuhide Yamasato11.1 Introduction 12511.2 General and taxonomic characters 12511.3 Phylogenetic affiliation of Marinilactibacillus species 12611.4 Physiological properties 12711.5 Differentiation of Marinilactibacillus from other related species 12711.6 Lactic acid fermentation and aerobic metabolism of glucose 12711.7 Ecology and isolation methods 12911.8 Description of the species of the genus Marinilactibacillus 13212 The genus Trichococcus 135Elena V. Pikuta and Richard B. Hoover12.1 Historical background and chronology of nomenclature for the Trichococcus species 13512.2 Definition of the genus Trichococcus 13612.3 Relationship to other genera within the Carnobacteriaceae and other LAB families 13612.4 Future taxonomic perspectives 13912.5 Techniques and growth requirements for cultivation of Trichococcus species 13912.6 Biodiversity 13912.7 Importance of the genus and particular species 14012.8 Species descriptions 14113 The genus Alkalibacterium 147Isao Yumoto, Kikue Hirota and Kenji Nakajima13.1 Introduction 14713.2 Taxonomy 14813.3 Description of the genus 14813.4 Enrichment and isolation procedures 14813.5 Natural habitats 14913.6 Acid production 15013.7 Identification of Alkalibacterium species 15013.8 Overview of the current situation for this genus 15013.9 Description of species 15313.10 Concluding remarks 15614 Minor genera of the Carnobacteriaceae: Allofustis, Alloiococcus, Atopobacter, Atopococcus, Atopostipes, Bavariicoccus, Desemzia, Dolosigranulum, Granulicatella, Isobaculum and Lacticigenium 159Ulrich Schillinger and Akihito Endo14.1 Introduction 15914.2 Taxonomy 15914.3 Biodiversity of each genus 16214.4 Practical importance 16314.5 Species descriptions 164Section III The family Enterococcaceae 171Pavel Švec and Charles M.A.P. Franz15 The genus Enterococcus 175Pavel Švec and Charles M.A.P. Franz15.1 Historical background and chronology of nomenclature 17515.2 Phenotypic differentiation of the genus Enterococcus 17815.3 Genotypic delineation of the genus Enterococcus 17815.4 Phylogenetic structure within the genus Enterococcus 17915.5 Isolation and cultivation 17915.6 Identification of Enterococcus spp. 17915.7 Importance of the genus and particular species 18215.8 Species of the genus Enterococcus 18616 The genus Tetragenococcus 213Annelies Justè, Bart Lievens, Hans Rediers and Kris A. Willems16.1 Introduction 21316.2 Phenotypic characteristics of the genus Tetragenococcus 21516.3 Genotypic characteristics of the genus Tetragenococcus 21716.4 Industrial relevance of the genus Tetragenococcus 22116.5 Description of species 22217 The genus Vagococcus 229Paul A. Lawson17.1 Introduction and historical background 22917.2 Description of the genus Vagococcus 22917.3 Differentiation of Vagococcus species from other genera 23017.4 Differentiation of species of the genus Vagococcus from one another 23117.5 Isolation, cultivation, ecology and medical importance 23117.6 Species descriptions 23218 Minor genera of the Enterococcaceae (Catellicoccus, Melissococcus and Pilibacter) 239Leon M.T. Dicks, Akihito Endo and Carol A. Van Reenen18.1 Introduction 23918.2 Phylogeny 23918.3 Morphology 24018.4 Growth characteristics 24018.5 Practical importance 24118.6 Description of species 241Section IV The family Lactobacillaceae 245Giovanna E. Felis and Bruno Pot19 The genus Lactobacillus 249Bruno Pot, Giovanna E. Felis, Katrien De Bruyne, Effie Tsakalidou, Konstantinos Papadimitriou,Jørgen Leisner and Peter Vandamme19.1 Historical background 24919.2 Lactobacillus metabolism 25019.3 The taxonomy of the genus Lactobacillus 28219.4 The current phylogenetic structure of the genus Lactobacillus 28619.5 Food and health applications of the genus Lactobacillus 29319.6 Short descriptions of the validly published species of the genus Lactobacillus 29419.7 Lactobacillus species awaiting validation pending publication of the manuscript (March 2013) 32719.8 Lactobacillus species and subspecies that have been renamed after their original description 32919.9 Lactobacillus species that have never been validly named, but whose names nonetheless appear in the literature, and their current names 33520 The genus Paralactobacillus 355Jørgen J. Leisner and Bruno Pot20.1 Introduction 35520.2 Defining the genus as phenotype and genotype 35520.3 Biodiversity within the genus and species based on phenotype 35620.4 Importance of the genus and particular species 35620.5 Description of species 35721 The genus Pediococcus 359Charles M.A.P. Franz, Akihito Endo, Hikmate Abriouel, Carol A. Van Reenen, Antonio Gálvez and Leon M.T. Dicks21.1 Historical background and chronology of nomenclature 35921.2 Phenotypic differentiation of the genus Pediococcus 36021.3 Genotypic delineation of the genus Pediococcus 36021.4 Phylogenetic structure within the genus Pediococcus 36121.5 Isolation and cultivation 36221.6 Identification of Pediococcus spp 36221.7 Importance of the genus and particular species 36521.8 Species of the genus Pediococcus 366Section V The family Leuconostocaceae 377Akihito Endo, Leon M.T. Dicks, Johanna Björkroth and Wilhelm H. Holzapfel22 The genus Fructobacillus 381Akihito Endo and Leon M.T. Dicks22.1 Introduction 38122.2 Phylogenetic relationships 38122.3 Morphology 38322.4 Biochemical characteristics 38322.5 Physiological characteristics 38622.6 Habitat 38622.7 Species in the genus Fructobacillus 38623 The genus Leuconostoc 391Johanna Björkroth, Leon M.T. Dicks, Akihito Endo and Wilhelm H. Holzapfel23.1 Historical background, chronology of nomenclature and relationship to other LAB 39123.2 Definition of the genus as phenotype 39223.3 Biodiversity within the genus based on phenotype 39323.4 Genomic studies and genotyping of Leuconostoc 39323.5 Importance of the genus and particular Leuconostoc species 39423.6 Description of species of the genus Leuconostoc 39524 The genus Oenococcus 405Akihito Endo and Leon M.T. Dicks24.1 Introduction 40524.2 Phylogeny and evolution 40524.3 Morphology 40624.4 Growth characteristics 40724.5 Intraspecies diversity 40924.6 Practical importance 41024.7 Stress response 41024.8 Description of species in the genus Oenococcus 41225 The genus Weissella 417Johanna Björkroth, Leon M.T. Dicks and Akihito Endo25.1 Historical background, chronology of nomenclature and relationship to other LAB 41725.2 Defining the genus as phenotype and genotype 41725.3 Biodiversity within the genus and within particular species based on phenotype 41925.4 Importance of the genus and particular species 41925.5 Descriptions of species in the genus Weisella 42126 The genus Lactococcus 42Wonyong Kim26.1 Introduction 42926.2 Defining the genus as phenotype and genotype 42926.3 Biodiversity within the genus based on phenotype 43326.4 Biodiversity within species based on phenotype 43426.5 Importance of the genus Lactococcus and species 43626.6 Description of species of the genus Lactococcus 437Section VI The family Streptococcaceae 445Maret du Toit, Melanie Huch, Gyu-Sung Cho and Charles M.A.P. Franz27 The genus Lactovum 447Harold L. Drake27.1 Introduction 44727.2 Phylogeny and taxonomy of Lactovum 44727.3 Morphology of Lactovum 44827.4 Soil: the origin of Lactovum 44927.5 Growth properties and substrate range of Lactovum 44927.6 Physiology of Lactovum 45127.7 Genus description 45227.8 Conclusion 45328 The genus Streptococcus 457Maret du Toit, Melanie Huch, Gyu-Sung Cho and Charles M.A.P. Franz28.1 Historical background and chronology of nomenclature 45728.2 Phenotypic differentiation of the genus Streptococcus 45828.3 Genotypic delineation of the genus Streptococcus 45828.4 Phylogenetic structure within the genus Streptococcus 45928.5 Isolation and cultivation 46528.6 Identification of Streptococcus spp. 46628.7 Importance of the genus and particular species 47528.8 Species of the genus Streptococcus 476Section VII Physiologically ‘related’ genera 507Wilhelm H. Holzapfel and Brian J.B. Wood29 The genera Bifidobacterium, Parascardovia and Scardovia 509Paola Mattarelli and Bruno Biavati29.1 Historical background 50929.2 Taxonomy of the bifidobacteria 51429.3 Ecology 52129.4 Health benefits 52229.5 Industrial applications 52329.6 Other applications 52329.7 Description of species 52429.8 Bifidobacterium: concluding remarks 53429.9 The genera Parascardovia and Scardovia 53430 The genus Sporolactobacillus 543Stephanie Doores30.1 Introduction 54330.2 Defining the genus as phenotype and genotype 54430.3 Importance of the genus and particular species 54730.4 Description of species of the genus Sporolactobacillus 54831 The genera Bacillus, Geobacillus and Halobacillus 555Hikmate Abriouel, Nabil Benomar, Melanie Huch, Charles M.A.P. Franz and Antonio Gálvez31.1 Introduction 55531.2 The genus Bacillus 55631.3 Related genera in the family Bacillaceae 56331.4 Food, health and environmental applications 56431.5 Concluding remarks 56532 The genera Halolactibacillus and Paraliobacillus 571Kazuhide Yamasato and Morio Ishikawa32.1 Introduction 57132.2 The genus Halolactibacillus 57132.3 Paraliobacillus ryukyuensis 578Appendix: Guidelines for characterizing LAB, bifidobacteria and related genera for taxonomic purposes 583Paola Mattarelli, Bruno Biavati, Walter Hammes and Wilhelm H. HolzapfelA.1 Introduction 583A.2 Phenotypic criteria 584A.3 Genotypic criteria 588A.4 Additional criteria 589A.5 Concluding remarks 591Index 593

"the current book is a very useful benchmark 'comprising well-crafted overviews of current developments' in lactic acid bacterial biodiversity and taxonomy." (Beneficial Microbes 2016)