Table of Contents

List of Contributors xiii

Preface xviii

1. Updates on Metabolism in Lactic Acid Bacteria in Light of “Omic” Technologies 1
Magdalena Kowalczyk, Baltasar Mayo, María Fernández, and Tamara Aleksandrzak-Piekarczyk

1.1. Sugar Metabolism 1

1.1.1. Practical Aspects of Sugar Catabolism 3

1.2. Citrate Metabolism and Formation of Aroma Compounds 4

1.2.1. Citrate Transport 4

1.2.2. Conversion of Citrate into Pyruvate and Production of Aroma Compounds 6

1.2.3. Conversion of Citrate into Succinate 6

1.2.4. Bioenergetics of Citrate Metabolism 6

1.3. The Proteolytic System of Lactic Acid Bacteria 6

1.3.1. Protein Degradation 7

1.3.2. Peptidases 8

1.3.3. Technological Applications of the Proteolytic System 10

1.3.4. Amino Acid Catabolism 10

1.4. LAB Metabolism in Light of Genomics Comparative Genomics and Metagenomics 12

1.5. Novel Aspects of Metabolism Regulation in the Post-genomic Age 12

1.6. Functional Genomics and Metabolism 16

1.6.1. Transcriptomics Proteomics and Metabolomics 16

1.6.2. Global Phenotypic Characterization of Microbial Cells 17

1.7. Systems Biology of LAB 17

Acknowledgments 18

References 18

2. Systematics of Lactic Acid Bacteria: Current Status 25
Giovanna E. Felis, Elisa Salvetti, and Sandra Torriani

2.1. Families and Genera of Lactic Acid Bacteria 25

2.2. A Focus on the Family Lactobacillaceae 27

2.3. Taxonomic Tools in the Genomic Era 29

References 30

3. Genomic Evolution of Lactic Acid Bacteria: From Single Gene Function to the Pan-genome 32
Grace L. Douglas, M. Andrea Azcarate-Peri,l and Todd R. Klaenhammer

3.1. The Genomics Revolution 32

3.2. Genomic Adaptations of LAB to the Environment 33

3.2.1. LAB Evolution in the Dairy Environment 33

3.2.2. LAB Evolution in Vegetable and Meat Fermentations 34

3.2.3. Fast-evolving LAB 35

3.2.4. LAB in the GI Tract 35

3.3. “Probiotic Islands”? 36

3.4. Stress Resistance and Quorum Sensing Mechanisms 39

3.5. The Impact of Genome Sequencing on Characterization Taxonomy and Pan-genome Development of
Lactic Acid Bacteria 40

3.6. Functional Genomic Studies to Unveil Novel LAB Utilities 45

3.7. Conclusions 47

References 47

4. Lactic Acid Bacteria: Comparative Genomic Analyses of Transport Systems 55
Graciela L. Lorca, Taylor A. Twiddy, and Milton H. Saier Jr.

4.1. Introduction 55

4.2. Channel-forming Proteins 56

4.3. The Major Facilitator Superfamily 59

4.4. Other Large Superfamilies of Secondary Carriers 60

4.5. ABC Transporters 64

4.6. Heavy Metal Transporters 65

4.7. P-type ATPases in Prokaryotes 68

4.8. The Prokaryote-specific Phosphotransferase System (PTS) 68

4.9. Multidrug Resistance Pumps 71

4.10. Nutrient Transport in LAB 71

4.11. Conclusions and Perspectives 72

Note 73

Acknowledgments 73

References 73

5. Novel Developments in Bacteriocins from Lactic Acid Bacteria 80
Ingolf F. Nes, Christina Gabrielsen, Dag A. Brede, and Dzung B. Diep

5.1. Introduction 80

5.2. Characteristics and Classification of Bacteriocins 80

5.2.1. Class Ia: Lantibiotics 81

5.2.2. Class II: The Non-lantibiotics 81

5.3. Mode of Action 84

5.4. Bacteriocin Resistance 86

5.5. Applications 88

5.5.1. Opportunities and Hurdles in Application of Bacteriocins 88

5.5.2. Application of Bacteriocins in Medical-related and Personal Hygiene Products 88

5.5.3. Bacteriocin-producing Probiotics 90

5.6. Future Perspectives 92

References 93

6. Bacteriophages of Lactic Acid Bacteria and Biotechnological Tools 100
Beatriz Martínez, Pilar García, Ana Rodríguez, Mariana Piuri, and Raúl R. Raya

6.1. Introduction 100

6.2. Bacteriophages of Lactic Acid Bacteria 101

6.2.1. Classification of Lactococcal Phages 103

6.3. Antiphage Strategies 103

6.3.1. Natural Mechanisms of Phage Resistance 103

6.3.2. Genetically Engineered Antiphage Systems 105

6.4. Phage-Based Molecular Tools 106

6.4.1. Phage Integrases and Integration Vectors 106

6.4.2. CRISPR Applications 108

6.4.3. Recombineering 110

6.5. LAB Phages as Biocontrol Tools 113

6.6. Conclusions 113

References 113

7. Lactic Acid Bacteria and the Human Intestinal Microbiome 120
François P. Douillard and Willem M. de Vos

7.1. Introduction 120

7.2. Ecology of the Human Intestinal Tract 121

7.2.1. The Human Microbiome in the Upper and Lower Intestinal Tract 121

7.2.2. Lactic Acid Bacteria Associated with the Human Intestine 122

7.2.3. Metagenomic Studies of the Intestine in Relation to LAB 123

7.3. A Case Study: The Lactobacillus rhamnosus Species 124

7.3.1. Genomic Diversity of Lact. rhamnosus and Intestinal Adaptation 124

7.3.2. Lact. rhamnosus Metabolism and Adaptation to the Intestine 126

7.3.3. Host Interaction Factors in Lact. rhamnosus 127

7.3.4. The Lact. rhamnosus Species: Autochthonous or Allochthonous in the Human Intestine? 127

7.4. Concluding Perspectives and Future Directions 129

Acknowledgments 130

References 130

8. Probiotics and Functional Foods in Immunosupressed Hosts 134
Ivanna Novotny Nuñez, Martin Manuel, Palomar Alejandra de Moreno de LeBlanc, Carolina Maldonado Galdeano, and Gabriela Perdigón

8.1. Introduction 134

8.2. Probiotic Fermented Milk in a Malnutrition Model 135

8.3. Probiotic Administration in Stress Process 138

8.4. Conclusions 140

Acknowledgments 141

References 141

9. Lactic Acid Bacteria in Animal Production and Health 144
Damien Bouchard, Sergine Even, and Yves Le Loir

9.1. Introduction 144

9.2. Lactic Acid Bacteria and Probiotics 145

9.3. Classifications and Regulatory Criteria of Probiotics in Animal Health 146

9.4. Probiotic LAB and Animal Production Sectors 147

9.4.1. Probiotics in Ruminants 147

9.4.2. Probiotics in Pigs 150

9.4.3. Probiotics in Poultry 152

9.5. Conclusions 154

References 154

10. Proteomics for Studying Probiotic Traits 159
Rosa Anna Siciliano and Maria Fiorella Mazzeo

10.1. Introduction 159

10.2. Mass Spectrometric Methodologies in Proteomics 160

10.2.1. The Classical Approach: 2-DE Separation and Protein Identification by Mass Spectrometry 160

10.2.2. Gel-Free Proteomic Approaches 160

10.3. Proteomics for Studying Molecular Mechanisms of Probiotic Action 161

10.3.1. Adaptation Mechanisms to the GIT Environment 161

10.3.2. Adhesion Mechanisms to the Host Mucosa 162

10.3.3. Molecular Mechanisms of Probiotic Immunomodulatory Effects 164

10.3.4. Probiotics and Prebiotics 164

10.4. Concluding Remarks and Future Directions 165

References 166

11. Engineering Lactic Acid Bacteria and Bifidobacteria for Mucosal Delivery of Health Molecules 170
Thibault Allain, Camille Aubry, Jane M. Natividad, Jean-Marc Chatel, Philippe Langella, and Luis G. Bermúdez-Humarán

11.1. Introduction 170

11.2. Lactococcus lactis: A Pioneer Bacterium 171

11.3. Lactobacillus spp. as a Delivery Vector 171

11.4. Bifidobacteria as a New Live Delivery Vehicle 171

11.5. Engineering Genetic Tools for Protein and DNA Delivery 172

11.5.1. Cloning Vectors 172

11.5.2. Expression Systems 173

11.6. Therapeutic Applications 176

11.6.1. Inflammatory Bowel Disease (IBD) 176

11.6.2. Anti-protease Enzyme-producing LAB: The Tole of Elafin 176

11.6.3. Antioxidant Enzyme-producing Lactococci and Lactobacilli 177

11.7. Allergy 178

11.7.1. Use of LAB in Food Allergy 178

11.7.2. Allergic Airways Diseases 179

11.8. Autoimmune Diseases 180

11.8.1. Type 1 Diabetes Mellitus 180

11.8.2. Celiac Disease 180

11.9. Infectious Diseases 181

11.9.1. Mucosal Delivery of Bacterial Antigens 181

11.9.2. Mucosal Delivery of Viral Antigens 181

11.9.3. Parasitic Diseases 183

References 184

12. Lactic Acid Bacteria for Dairy Fermentations: Specialized Starter Cultures to Improve Dairy Products 191
Domenico Carminati, Giorgio Giraffa, Miriam Zago, Mariángeles Briggiler Marcó, Daniela Guglielmotti, Ana
Binetti, and Jorge Reinheimer

12.1. Introduction 191

12.2. Adjunct Cultures 191

12.2.1. Ripening Cultures 192

12.2.2. Protective Cultures 193

12.2.3. Probiotic Cultures 195

12.2.4. Exopolysaccharide-producing Starters 196

12.3. Phage-Resistant Starters 199

12.4. New Sources of Starter Strains 201

12.5. Conclusions 202

References 203

13. Lactobacillus sakei in Meat Fermentation 209
Marie-Christine Champomier-Vergès and Monique Zagorec

13.1. Introduction 209

13.2. Genomics and Diversity of the Species Lactobacillus sakei 210

13.3. Post-genomic Vision of Meat Fitness Traits of Lactobacillus sakei 212

13.3.1. Energy Sources 212

13.3.2. Stress Response 213

13.4. Conclusions 214

References 214

14. Vegetable and Fruit Fermentation by Lactic Acid Bacteria 216
Raffaella Di Cagno, Pasquale Filannino, and Marco Gobbetti

14.1. Introduction 216

14.2. Lactic Acid Bacteria Microbiota of Raw Vegetables and Fruits 216

14.3. Fermentation of Vegetable Products 218

14.3.1. Spontaneous Fermentation 218

14.3.2. The Autochthonous Starters 218

14.4. Main Fermented Vegetable Products 221

14.4.1. Sauerkrauts 221

14.4.2. Kimchi 222

14.4.3. Pickled Cucumbers 223

14.5. Physiology and Biochemistry of LAB during Vegetable and Fruit Fermentation 223

14.5.1. Metabolic Adaptation by LAB during Plant Fermentation 224

14.6. Food Phenolic Compounds: Antimicrobial Activity and Microbial Responses 224

14.6.1. Effect of Phenolics on the Growth and Viability of LAB 224

14.6.2. Metabolism of Phenolics by LAB 226

14.7. Health-promoting Properties of Fermented Vegetables and Fruits 226

14.8. Alternative Sources of Novel Probiotics Candidates 226

14.9. Vehicles for Delivering Probiotics 228

14.10. Conclusions 229

References 229

15. Lactic Acid Bacteria and Malolactic Fermentation in Wine 231
Aline Lonvaud-Funel

15.1. Introduction 231

15.2. The Lactic Acid Bacteria of Wine 231

15.2.1. Origin 231

15.2.2. Species 232

15.2.3. Identification 232

15.2.4. Typing at Strain Level 233

15.2.5. Detection of Specific Strains 233

15.3. The Oenococcus Oeni Species 233

15.4. Evolution of Lactic Acid Bacteria during Winemaking 234

15.4.1. Interactions between Wine Microorganisms 235

15.4.2. Environmental Factors 236

15.5. Lactic Acid Bacteria Metabolism and its Impact on Wine Quality 237

15.5.1. Sugars 237

15.5.2. Carboxylic Acids 237

15.5.3. Amino Acids 240

15.5.4. Other Metabolisms with Sensorial Impact 241

15.6. Controlling the Malolactic Fermentation 242

15.7. Conclusions 243

References 244

16. The Functional Role of Lactic Acid Bacteria in Cocoa Bean Fermentation 248
Luc De Vuyst and Stefan Weckx

16.1. Introduction 248

16.2. Cocoa Crop Cultivation and Harvest 249

16.3. The Cocoa Pulp or Fermentation Substrate 250

16.4. Fresh Unfermented Cocoa Beans 251

16.5. Cocoa Bean Fermentation 252

16.5.1. Rationale 252

16.5.2. Farming Practices 253

16.6. Succession of Microorganisms during Cocoa Bean Fermentation 256

16.6.1. The Spontaneous Three-phase Cocoa Bean Fermentation Process 256

16.6.2. Yeast Fermentation 257

16.6.3. LAB Fermentation 260

16.6.4. AAB Fermentation 264

16.7. Biochemical Changes in the Cocoa Beans during Fermentation and Drying 266

16.8. Optimal Fermentation Course and End of Fermentation 268

16.9. Further Processing of Fermented Cocoa Beans 269

16.9.1. Drying of Fermented Cocoa Beans 269

16.9.2. Roasting of Fermented Dry Cocoa Beans 270

16.10. Use of Starter Cultures for Cocoa Bean Fermentation 271

16.10.1. Rationale 271

16.10.2. Experimental Use of Cocoa Bean Starter Cultures 271

16.11. Concluding Remarks 273

References 273

17. B-Group Vitamins Production by Probiotic Lactic Acid Bacteria 279
Jean Guy LeBlanc, Jonathan Emiliano Laiño, Marianela Juárez del Valle, Graciela Savoy de Giori, Fernando
Sesma, and María Pía Taranto

17.1. Introduction 279

17.2. B-Group Vitamins 280

17.2.1. Riboflavin (Vitamin B2) 281

17.2.2. Folates (Vitamin B9) 284

17.3. Probiotics In Situ 286

17.3.1. Vitamin B12 (Cobalamin) 288

17.3.2. Cobalamin Biosynthesis by Lactobacillus reuteri 289

17.4. Conclusions 291

Acknowledgments 292

References 292

18. Nutraceutics and High Value Metabolites Produced by Lactic Acid Bacteria 297
Elvira M. Hebert, Graciela Savoy de Giori, and Fernanda Mozzi

18.1. Introduction 297

18.2. Nutraceutics 298

18.2.1. Low-calorie Sugars 298

18.2.2. Short-Chain Fatty Acids 300

18.2.3. Conjugated Linoleic Acid (CLA) 301

18.2.4. Bioactive Peptides 301

18.2.5. Gamma-aminobutyric Acid (GABA) 303

18.2.6. Vitamins 305

18.3. Exopolysaccharides 306

18.4. Commodity Chemicals 307

18.5. Conclusions 308

References 308

19. Production of Flavor Compounds by Lactic Acid Bacteria in Fermented Foods 314
Anne Thierry, Tomislav Pogačic, Magalie Weber, and Sylvie Lortal

19.1. Introduction 314

19.2. Flavor and Aroma Compounds 315

19.2.1. Volatile Compounds: Diversity Analytical Methods 315

19.2.2. Contribution of Volatile Aroma Compounds to Flavor 316

19.2.3. Origin of Aroma Compounds 316

19.3. LAB of Fermented Foods and their Role in Flavor Formation 316

19.3.1. Biochemical Processes of Flavor Compound Formation in Food and Potential of LAB 324

19.3.2. Flavor Compounds Produced from Carbohydrate Fermentation by LAB 324

19.3.3. Flavor Compounds from Amino Acid Conversion by LAB 326

19.3.4. Flavor Compounds from Lipids in LAB 327

19.3.5. Synthesis of Esters 328

19.3.6. Interspecies and Intraspecies Variations of Aroma Compound Production 328

19.4. Biotic and Abiotic Factors Modulating the Contribution of LAB to Flavor Formation 331

19.4.1. General Scheme of Flavor Formation in Fermented Foods In Situ 331

19.4.2. Factors Modulating the Expression of the Flavor-related Activities of LAB 332

19.4.3. Factors Determining the Real Contribution of LAB to Food Flavor 333

19.5. Conclusions and Research Perspectives 333

References 334

20. Lactic Acid Bacteria Biofilms: From their Formation to their Health and Biotechnological Potential 341
Jean-Christophe Piard and Romain Briandet

20.1. Lactic Acid Bacteria Biofilms are Ubiquitous in a Wide Variety of Environments from Nature to
Domesticated Settings 341

20.2. Biofilm Life Cycle and Bacterial Factors Involved in LAB Biofilm Lifestyle 346

20.3. Health and Biotechnological Potential of LAB Biofilms and Underlying Mechanisms 352

20.4. Conclusions 354

Acknowledgments 355

References 355

Index 362