Biotechnology of lactic acid bacteria : novel applications

395 Pages·2010·9.93 MB·English

by  Mozzi

Biotechnology of Lactic Acid
Bacteria
Novel Applications

Biotechnology of Lactic Acid
Bacteria
Novel Applications
Second Edition
Edited by
Fernanda Mozzi, Raúl R. Raya, and Graciela M. Vignolo
This edition first published 2016
© 2016 by John Wiley & Sons, Ltd.
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Set in 9.5/11.5pt Times by SPi Global, Pondicherry, India
1 2016
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
v
vi Contents
3. Genomic Evolution of Lactic Acid Bacteria: From Single Gene Function to the
Pan‐genome, 32
Grace L. Douglas, M. Andrea Azcarate‐Peril, 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
Contents vii
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
viii Contents
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