Lactic Acid Bacteria Lactic Acid Bacteria Biodiversity and Taxonomy Edited by Wilhelm H. Holzapfel School of Life Sciences, Handong Global University, Pohang, Gyeongbuk, South Korea; Insheimer Strasse 27, Rohrbach, Germany Brian J.B. Wood Formerly Reader in Applied Microbiology, Strathclyde Institute for Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, Scotland, UK This edition first published 2014 © 2014 by John Wiley & Sons, Ltd Registered office: John Wiley & Sons, Ltd, The Atrium, Southern Gate, Chichester, West Sussex, PO19 8SQ, UK Editorial offices: 9600 Garsington Road, Oxford, OX4 2DQ, UK The Atrium, Southern Gate, Chichester, West Sussex, PO19 8SQ, UK 111 River Street, Hoboken, NJ 07030-5774, USA For details of our global editorial offices, for customer services and for information about how to apply for permission to reuse the copyright material in this book please see our website at www.wiley.com/wiley-blackwell. 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Limit of Liability/Disclaimer of Warranty: While the publisher and author(s) have used their best efforts in preparing this book, they make no representations or warranties with respect to the accuracy or completeness of the contents of this book and specifically disclaim any implied warranties of merchantability or fitness for a particular purpose. It is sold on the understanding that the publisher is not engaged in rendering professional services and neither the publisher nor the author shall be liable for damages arising herefrom. If professional advice or other expert assistance is required, the services of a competent professional should be sought. Library of Congress Cataloging-in-Publication Data Lactic acid bacteria : biodiversity and taxonomy / edited by Wilhelm Holzapfel. pages cm Includes bibliographical references and index. ISBN 978-1-4443-3383-1 (cloth) 1. Lactic acid bacteria. 2. Biodiversity. 3. Microbial diversity. 4. Lactic acid bacteria – Classification. 5. Lactic acid bacteria – Physiology. 6. Microbiological chemistry. 7. Lactic acid bacteria – Molecular aspects. I. Holzapfel, W. H. QR121.L3335 2014 579.3′5– dc23 2013028930 A catalogue record for this book is available from the British Library. Wiley also publishes its books in a variety of electronic formats. Some content that appears in print may not be available in electronic books. Cover image: Salted Peppers © Drbouz/ Istock food industry manufacturing interior © picsfive/ Istock Sourdough © karma_ pema/ Istock bacillus bacteria © sgame/ Istock Cheese © IvonneW/ Istock Meat-Salami © Floortje/ Istock Yoghurt Jar © AndreaAstes/ Istock Cover design by www.hisandhersdesign.co.uk Set in 10/12pt TimesTen by Laserwords Private Limited, Chennai, India 12014 Contents 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 vi CONTENTS 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 CONTENTS vii 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 viii CONTENTS 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.