List of Contributors xiii
Preface xviii
1. Updates on Metabolism in Lactic Acid Bacteria in Light of “Omic” Technologies 1
Magdalena Kowalczyk, Baltasar Mayo, Maria Fernandez, 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 Martinez, Pilar Garcia, Ana Rodriguez, Mariana Piuri, and Raul 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 Nunez, Martin Manuel, Palomar Alejandra de Moreno de LeBlanc, Carolina Maldonado Galdeano, and Gabriela Perdigon
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. Bermudez-Humaran
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, Mariangeles Briggiler Marco, 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-Verges 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 Laino, Marianela Juarez del Valle, Graciela Savoy de Giori, Fernando
Sesma, and Maria Pia 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 Pogac?ic, 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
