1. Updates on Metabolism in Lactic Acid Bacteria in Light of “Omic” Technologies
Magdalena Kowalczyk, Baltasar Mayo, María Fernández, and Tamara Aleksandrzak-Piekarczyk
1.1. Sugar Metabolism
1.1.1. Practical Aspects of Sugar Catabolism
1.2. Citrate Metabolism and Formation of Aroma Compounds
1.2.1. Citrate Transport
1.2.2. Conversion of Citrate into Pyruvate and Production of Aroma Compounds
1.2.3. Conversion of Citrate into Succinate
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1. Updates on Metabolism in Lactic Acid Bacteria in Light of “Omic” Technologies
Magdalena Kowalczyk, Baltasar Mayo, María Fernández, and Tamara Aleksandrzak-Piekarczyk
1.1. Sugar Metabolism
1.1.1. Practical Aspects of Sugar Catabolism
1.2. Citrate Metabolism and Formation of Aroma Compounds
1.2.1. Citrate Transport
1.2.2. Conversion of Citrate into Pyruvate and Production of Aroma Compounds
1.2.3. Conversion of Citrate into Succinate
1.2.4. Bioenergetics of Citrate Metabolism
1.3. The Proteolytic System of Lactic Acid Bacteria
1.3.1. Protein Degradation
1.3.2. Peptidases
1.3.3. Technological Applications of the Proteolytic System
1.3.4. Amino Acid Catabolism
1.4. LAB Metabolism in Light of Genomics, Comparative Genomics and Metagenomics
1.5. Novel Aspects of Metabolism Regulation in the Post-genomic Age
1.6. Functional Genomics and Metabolism
1.6.1. Transcriptomics Proteomics and Metabolomics
1.6.2. Global Phenotypic Characterization of Microbial Cells
1.7. Systems Biology of LAB
2. Systematics of Lactic Acid Bacteria: Current Status
Giovanna E. Felis, Elisa Salvetti, and Sandra Torriani
2.1. Families and Genera of Lactic Acid Bacteria
2.2. A Focus on the Family Lactobacillaceae
2.3. Taxonomic Tools in the Genomic Era
3. Genomic Evolution of Lactic Acid Bacteria: From Single Gene Function to the Pan-genome
Grace L. Douglas, M. Andrea Azcarate-Peri,l and Todd R. Klaenhammer
3.1. The Genomics Revolution
3.2. Genomic Adaptations of LAB to the Environment
3.2.1. LAB Evolution in the Dairy Environment
3.2.2. LAB Evolution in Vegetable and Meat Fermentations
3.2.3. Fast-evolving LAB
3.2.4. LAB in the GI Tract
3.3. “Probiotic Islands”?
3.4. Stress Resistance and Quorum Sensing Mechanisms
3.5. The Impact of Genome Sequencing on Characterization Taxonomy and Pan-genome Development of
Lactic Acid Bacteria
3.6. Functional Genomic Studies to Unveil Novel LAB Utilities
4. Lactic Acid Bacteria: Comparative Genomic Analyses of Transport Systems
Graciela L. Lorca, Taylor A. Twiddy, and Milton H. Saier Jr.
4.1. Introduction
4.2. Channel-forming Proteins
4.3. The Major Facilitator Superfamily
4.4. Other Large Superfamilies of Secondary Carriers
4.5. ABC Transporters
4.6. Heavy Metal Transporters
4.7. P-type ATPases in Prokaryotes
4.8. The Prokaryote-specific Phosphotransferase System (PTS)
4.9. Multidrug Resistance Pumps
4.10. Nutrient Transport in LAB
4.11. Conclusions and Perspectives
5. Novel Developments in Bacteriocins from Lactic Acid Bacteria
Ingolf F. Nes, Christina Gabrielsen, Dag A. Brede, and Dzung B. Diep
5.1. Introduction
5.2. Characteristics and Classification of Bacteriocins
5.2.1. Class Ia: Lantibiotics
5.2.2. Class II: The Non-lantibiotics
5.3. Mode of Action
5.4. Bacteriocin Resistance
5.5. Applications
5.5.1. Opportunities and Hurdles in Application of Bacteriocins
5.5.2. Application of Bacteriocins in Medical-related and Personal Hygiene Products
5.5.3. Bacteriocin-producing Probiotics
5.6. Future Perspectives
6. Bacteriophages of Lactic Acid Bacteria and Biotechnological Tools
Beatriz Martínez, Pilar García, Ana Rodríguez, Mariana Piuri, and Raúl R. Raya
6.1. Introduction
6.2. Bacteriophages of Lactic Acid Bacteria
6.2.1. Classification of Lactococcal Phages
6.3. Antiphage Strategies
6.3.1. Natural Mechanisms of Phage Resistance
6.3.2. Genetically Engineered Antiphage Systems
6.4. Phage-Based Molecular Tools
6.4.1. Phage Integrases and Integration Vectors
6.4.2. CRISPR Applications
6.4.3. Recombineering
6.5. LAB Phages as Biocontrol Tools
6.6. Conclusions
7. Lactic Acid Bacteria and the Human Intestinal Microbiome
François P. Douillard and Willem M. de Vos
7.1. Introduction
7.2. Ecology of the Human Intestinal Tract
7.2.1. The Human Microbiome in the Upper and Lower Intestinal Tract
7.2.2. Lactic Acid Bacteria Associated with the Human Intestine
7.2.3. Metagenomic Studies of the Intestine in Relation to LAB
7.3. A Case Study: The Lactobacillus rhamnosus Species
7.3.1. Genomic Diversity of Lact. rhamnosus and Intestinal Adaptation
7.3.2. Lact. rhamnosus Metabolism and Adaptation to the Intestine
7.3.3. Host Interaction Factors in Lact. rhamnosus
7.3.4. The Lact. rhamnosus Species: Autochthonous or Allochthonous in the Human Intestine?
7.4. Concluding Perspectives and Future Directions
8. Probiotics and Functional Foods in Immunosupressed Hosts
Ivanna Novotny Nuñez, Martin Manuel Palomar, Alejandra de Moreno de LeBlanc, Carolina Maldonado Galdeano, and Gabriela Perdigón
8.1. Introduction
8.2. Probiotic Fermented Milk in a Malnutrition Model
8.3. Probiotic Administration in Stress Process
8.4. Conclusions
9. Lactic Acid Bacteria in Animal Production and Health
Damien Bouchard, Sergine Even, and Yves Le Loir
9.1. Introduction
9.2. Lactic Acid Bacteria and Probiotics
9.3. Classifications and Regulatory Criteria of Probiotics in Animal Health
9.4. Probiotic LAB and Animal Production Sectors
9.4.1. Probiotics in Ruminants
9.4.2. Probiotics in Pigs
9.4.3. Probiotics in Poultry
9.5. Conclusions
10. Proteomics for Studying Probiotic Traits
Rosa Anna Siciliano and Maria Fiorella Mazzeo
10.1. Introduction
10.2. Mass Spectrometric Methodologies in Proteomics
10.2.1. The Classical Approach: 2-DE Separation and Protein Identification by Mass Spectrometry
10.2.2. Gel-Free Proteomic Approaches
10.3. Proteomics for Studying Molecular Mechanisms of Probiotic Action
10.3.1. Adaptation Mechanisms to the GIT Environment
10.3.2. Adhesion Mechanisms to the Host Mucosa
10.3.3. Molecular Mechanisms of Probiotic Immunomodulatory Effects
10.3.4. Probiotics and Prebiotics
10.4. Concluding Remarks and Future Directions
11. Engineering Lactic Acid Bacteria and Bifidobacteria for Mucosal Delivery of Health Molecules
Thibault Allain, Camille Aubry, Jane M. Natividad, Jean-Marc Chatel, Philippe Langella, and Luis G. Bermúdez-Humarán
11.1. Introduction
11.2. Lactococcus lactis: A Pioneer Bacterium
11.3. Lactobacillus spp. as a Delivery Vector
11.4. Bifidobacteria as a New Live Delivery Vehicle
11.5. Engineering Genetic Tools for Protein and DNA Delivery
11.5.1. Cloning Vectors
11.5.2. Expression Systems
11.6. Therapeutic Applications
11.6.1. Inflammatory Bowel Disease (IBD)
11.6.2. Anti-protease Enzyme-producing LAB: The Tole of Elafin
11.6.3. Antioxidant Enzyme-producing Lactococci and Lactobacilli
11.7. Allergy
11.7.1. Use of LAB in Food Allergy
11.7.2. Allergic Airways Diseases
11.8. Autoimmune Diseases
11.8.1. Type 1 Diabetes Mellitus
11.8.2. Celiac Disease
11.9. Infectious Diseases
11.9.1. Mucosal Delivery of Bacterial Antigens
11.9.2. Mucosal Delivery of Viral Antigens
11.9.3. Parasitic Diseases
12. Lactic Acid Bacteria for Dairy Fermentations: Specialized Starter Cultures to Improve Dairy Products
Domenico Carminati, Giorgio Giraffa, Miriam Zago, Mariángeles Briggiler Marcó, Daniela Guglielmotti, Ana Binetti, and Jorge Reinheimer
12.1. Introduction
12.2. Adjunct Cultures
12.2.1. Ripening Cultures
12.2.2. Protective Cultures
12.2.3. Probiotic Cultures
12.2.4. Exopolysaccharide-producing Starters
12.3. Phage-Resistant Starters
12.4. New Sources of Starter Strains
12.5. Conclusions
13. Lactobacillus sakei in Meat Fermentation
Marie-Christine Champomier-Vergès and Monique Zagorec
13.1. Introduction
13.2. Genomics and Diversity of the Species Lactobacillus sakei
13.3. Post-genomic Vision of Meat Fitness Traits of Lactobacillus sakei
13.3.1. Energy Sources
13.3.2. Stress Response
13.4. Conclusions
14. Vegetable and Fruit Fermentation by Lactic Acid Bacteria
Raffaella Di Cagno, Pasquale Filannino, and Marco Gobbetti
14.1. Introduction
14.2. Lactic Acid Bacteria Microbiota of Raw Vegetables and Fruits
14.3. Fermentation of Vegetable Products
14.3.1. Spontaneous Fermentation
14.3.2. The Autochthonous Starters
14.4. Main Fermented Vegetable Products
14.4.1. Sauerkrauts
14.4.2. Kimchi
14.4.3. Pickled Cucumbers
14.5. Physiology and Biochemistry of LAB during Vegetable and Fruit Fermentation
14.5.1. Metabolic Adaptation by LAB during Plant Fermentation
14.6. Food Phenolic Compounds: Antimicrobial Activity and Microbial Responses
14.6.1. Effect of Phenolics on the Growth and Viability of LAB
14.6.2. Metabolism of Phenolics by LAB
14.7. Health-promoting Properties of Fermented Vegetables and Fruits
14.8. Alternative Sources of Novel Probiotics Candidates
14.9. Vehicles for Delivering Probiotics
14.10. Conclusions
15. Lactic Acid Bacteria and Malolactic Fermentation in Wine
Aline Lonvaud-Funel
15.1. Introduction
15.2. The Lactic Acid Bacteria of Wine
15.2.1. Origin
15.2.2. Species
15.2.3. Identification
15.2.4. Typing at Strain Level
15.2.5. Detection of Specific Strains
15.3. The Oenococcus Oeni Species
15.4. Evolution of Lactic Acid Bacteria during Winemaking
15.4.1. Interactions between Wine Microorganisms
15.4.2. Environmental Factors
15.5. Lactic Acid Bacteria Metabolism and its Impact on Wine Quality
15.5.1. Sugars
15.5.2. Carboxylic Acids
15.5.3. Amino Acids
15.5.4. Other Metabolisms with Sensorial Impact
15.6. Controlling the Malolactic Fermentation
15.7. Conclusions
16. The Functional Role of Lactic Acid Bacteria in Cocoa Bean Fermentation
Luc De Vuyst and Stefan Weckx
16.1. Introduction
16.2. Cocoa Crop Cultivation and Harvest
16.3. The Cocoa Pulp or Fermentation Substrate
16.4. Fresh Unfermented Cocoa Beans
16.5. Cocoa Bean Fermentation
16.5.1. Rationale
16.5.2. Farming Practices
16.6. Succession of Microorganisms during Cocoa Bean Fermentation
16.6.1. The Spontaneous Three-phase Cocoa Bean Fermentation Process
16.6.2. Yeast Fermentation
16.6.3. LAB Fermentation
16.6.4. AAB Fermentation
16.7. Biochemical Changes in the Cocoa Beans during Fermentation and Drying
16.8. Optimal Fermentation Course and End of Fermentation
16.9. Further Processing of Fermented Cocoa Beans
16.9.1. Drying of Fermented Cocoa Beans
16.9.2. Roasting of Fermented Dry Cocoa Beans
16.10. Use of Starter Cultures for Cocoa Bean Fermentation
16.10.1. Rationale
16.10.2. Experimental Use of Cocoa Bean Starter Cultures
16.11. Concluding Remarks
17. B-Group Vitamins Production by Probiotic Lactic Acid Bacteria
Jean Guy LeBlanc, Jonathan Emiliano Laiño, Marianela Juárez del Valle, Graciela Savoy de Giori, Fernando Sesma, and María Pía Taranto
17.1. Introduction
17.2. B-Group Vitamins
17.2.1. Riboflavin (Vitamin B2)
17.2.2. Folates (Vitamin B9)
17.3. Probiotics In Situ
17.3.1. Vitamin B12 (Cobalamin)
17.3.2. Cobalamin Biosynthesis by Lactobacillus reuteri
17.4. Conclusions
18. Nutraceutics and High Value Metabolites Produced by Lactic Acid Bacteria
Elvira M. Hebert, Graciela Savoy de Giori, and Fernanda Mozzi
18.1. Introduction
18.2. Nutraceutics
18.2.1. Low-calorie Sugars
18.2.2. Short-Chain Fatty Acids
18.2.3. Conjugated Linoleic Acid (CLA)
18.2.4. Bioactive Peptides
18.2.5. Gamma-aminobutyric Acid (GABA)
18.2.6. Vitamins
18.3. Exopolysaccharides
18.4. Commodity Chemicals
18.5. Conclusions
19. Production of Flavor Compounds by Lactic Acid Bacteria in Fermented Foods
Anne Thierry, Tomislav Pogačic, Magalie Weber, and Sylvie Lortal
19.1. Introduction
19.2. Flavor and Aroma Compounds
19.2.1. Volatile Compounds: Diversity Analytical Methods
19.2.2. Contribution of Volatile Aroma Compounds to Flavor
19.2.3. Origin of Aroma Compounds
19.3. LAB of Fermented Foods and their Role in Flavor Formation
19.3.1. Biochemical Processes of Flavor Compound Formation in Food and Potential of LAB
19.3.2. Flavor Compounds Produced from Carbohydrate Fermentation by LAB
19.3.3. Flavor Compounds from Amino Acid Conversion by LAB
19.3.4. Flavor Compounds from Lipids in LAB
19.3.5. Synthesis of Esters
19.3.6. Interspecies and Intraspecies Variations of Aroma Compound Production
19.4. Biotic and Abiotic Factors Modulating the Contribution of LAB to Flavor Formation
19.4.1. General Scheme of Flavor Formation in Fermented Foods In Situ
19.4.2. Factors Modulating the Expression of the Flavor-related Activities of LAB
19.4.3. Factors Determining the Real Contribution of LAB to Food Flavor
19.5. Conclusions and Research Perspectives
20. Lactic Acid Bacteria Biofilms: From their Formation to their Health and Biotechnological Potential
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
20.2. Biofilm Life Cycle and Bacterial Factors Involved in LAB Biofilm Lifestyle
20.3. Health and Biotechnological Potential of LAB Biofilms and Underlying Mechanisms
20.4. Conclusions
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