Chapter
1.2.1 - Application of Genomics and Molecular Markers
1.3 - Phenotypic and physiological characteristics
1.5 - Natural and bioactive compounds
Chapter 2 - Species in the Genus Bifidobacterium
2.2 - Historical background
2.3 - Brief guideline for new bifidobacterial species description
2.3.1 - Deposit of Strains into Public Culture Collections: Importance and Rules (Nagoya Protocol Compliance)
2.4 - New insights into bifidobacterial species ecology
2.5 - List of the species of the genus Bifidobacterium
2.5.1 - Bifidobacterium actinocoloniiforme
2.5.2 - Bifidobacterium aquikefiri
2.5.3 - Bifidobacterium adolescentis
2.5.4 - Bifidobacterium aerophilum
2.5.5 - Bifidobacterium aesculapii
2.5.6 - Bifidobacterium angulatum
2.5.7 - Bifidobacterium animalis
2.5.7.1 - Bifidobacterium animalis subsp. animalis
2.5.7.2 - Bifidobacterium animalis subsp. lactis
2.5.8 - Bifidobacterium asteroides
2.5.9 - Bifidobacterium avesanii
2.5.10 - Bifidobacterium biavatii
2.5.11 - Bifidobacterium bifidum
2.5.12 - Bifidobacterium bohemicum
2.5.13 - Bifidobacterium bombi
2.5.14 - Bifidobacterium boum
2.5.15 - Bifidobacterium breve
2.5.16 - Bifidobacterium callithricos
2.5.17 - Bifidobacterium catenulatum
2.5.18 - Bifidobacterium choerinum
2.5.19 - Bifidobacterium commune
2.5.20 - Bifidobacterium coryneforme
2.5.21 - Bifidobacterium crudilactis
2.5.22 - Bifidobacterium cuniculi
2.5.24 - Bifidobacterium eulemuris
2.5.25 - Bifidobacterium fecale
2.5.26 - Bifidobacterium gallicum
2.5.27 - Bifidobacterium gallinarum
2.5.28 - Bifidobacterium hapali
2.5.29 - Bifidobacterium indicum
2.5.30 - Bifidobacterium kashiwanohense
2.5.31 - Bifidobacterium lemurum
2.5.32 - Bifidobacterium longum
2.5.32.1 - Bifidobacterium longum subsp. longum
2.5.32.2 - Bifidobacterium longum subsp. infantis
2.5.32.3 - Bifidobacterium longum subsp. suis
2.5.32.4 - Bifidobacterium longum subsp. suillum
2.5.33 - Bifidobacterium magnum
2.5.34 - Bifidobacterium merycicum
2.5.35 - Bifidobacterium minimum
2.5.36 - Bifidobacterium mongoliense
2.5.37 - Bifidobacterium moukalabense
2.5.38 - Bifidobacterium myosotis
2.5.39 - Bifidobacterium pseudocatenulatum
2.5.40 - Bifidobacterium pseudolongum
2.5.40.1 - Bifidobacterium pseudolongum subsp. pseudolongum
2.5.40.2 - Bifidobacterium pseudolongum subsp. globosum
2.5.41 - Bifidobacterium psychraerophilum
2.5.42 - Bifidobacterium pullorum
2.5.43 - Bifidobacterium ramosum
2.5.44 - Bifidobacterium reuteri
2.5.45 - Bifidobacterium ruminantium
2.5.46 - Bifidobacterium saguini
2.5.47 - Bifidobacterium saeculare
2.5.48 - Bifidobacterium scardovii
2.5.49 - Bifidobacterium stellenboshense
2.5.50 - Bifidobacterium subtile
2.5.51 - Bifidobacterium thermoacidophilum
2.5.51.1 - Bifidobacterium thermacidophilum subsp. thermoacidophilum
2.5.51.2 - Bifidobacterium thermoacidophilum subsp. porcinum
2.5.52 - Bifidobacterium thermophilum
2.5.53 - Bifidobacterium tissieri
2.5.54 - Bifidobacterium tsurumiense
Chapter 3 - Related Genera Within the Family Bifidobacteriaceae
3.2 - Phenotypic characteristics
3.2.1 - Carbohydrate Fermentation and Enzyme Patterns
3.2.1.1 - Aeriscardovia aeriphila
3.2.1.2 - Alloscardovia omnicolens
3.2.1.3 - Alloscardovia macacae
3.2.1.4 - Alloscardovia criceti
3.2.1.5 - Bombiscardovia coagulans
3.2.1.6 - Neoscardovia arbecensis
3.2.1.7 - Parascardovia denticolens
3.2.1.8 - Pseudoscardovia suis
3.2.1.9 - Pseudoscardovia radai
3.2.1.10 - Scardovia inopinata
3.2.1.11 - Scardovia wiggsiae
3.3 - Phylogenetic Relationships
3.4 - Description of the minor genera of the Bifidobacteriaceae family and list of the species
3.4.1 - The Genus Aeriscardovia
3.4.1.1 - Aeriscardovia aeriphila
3.4.1.1.1 - Additional Information
3.4.2 - The Genus Alloscardovia
3.4.2.1 - Alloscardovia omnicolens
3.4.2.1.1 - Additional Information
3.4.2.2 - Alloscardovia macacae
3.4.2.3 - Alloscardovia criceti
3.4.2.3.1 - Additional Information
3.4.3 - The Genus Bombiscardovia
3.4.3.1 - Additional Information
3.4.3.2 - Bombiscardovia coagulans
3.4.4 - The Genus Neoscardovia
3.4.4.1 - Neoscardovia arbecensis
3.4.5 - The Genus Parascardovia
3.4.5.1 - Parascardovia denticolens
3.4.5.1.1 - Additional Information
3.4.6 - The Genus Pseudoscardovia
3.4.6.1 - Pseudoscardovia suis
3.4.6.2 - Pseudoscardovia radai
3.4.7 - The Genus Scardovia
3.4.7.1 - Scardovia inopinata
3.4.7.1.1 - Additional Information
3.4.7.2 - Scardovia wiggsiae
3.4.7.2.1 - Additional Information
Chapter 4 - Isolation, Cultivation, and Storage of Bifidobacteria
4.3.2 - Fermented Dairy Products
4.4.1 - Short-Term Methods
4.4.2 - Long-Term Methods
4.4.2.1 - Cryopreservation
4.4.3 - Methods for Drying Probiotics
Chapter 5 - Chemotaxonomic Features in the Bifidobacteriaceae Family
5.2 - Cell wall structure
5.2.1 - Peptidoglycan Structure
5.2.4 - Cell-Wall Polysaccharides
5.3 - Whole cell chemical compounds
5.3.1 - Fatty Acid Analysis
5.3.2 - Acetic and Lactic Acid Production
5.3.4 - Polyacrylamide Gel Electrophoresis
Chapter 6 - Nutritional Requirements of Bifidobacteria
6.1 - Characteristics of bifidobacteria and their metabolism
6.2 - Nutritional requirements
6.2.1 - Carbohydrate Sources
6.2.1.2 - Galactose and Galactooligosaccharides
6.2.1.3 - Fructose, Fructooligosaccharides, and Inulin
6.2.1.4 - Xylose and Xylooligosaccharides
6.2.1.5 - Arabinose, Arabinoxylans, and Arabinooligosaccharides
6.2.1.6 - Milk Oligosaccharides
6.2.2 - Regulation of Carbohydrate Metabolism
6.2.3 - Other Macronutrients
6.3 - In vitro cultivation
Chapter 7 - Stress Responses of Bifidobacteria: Oxygen and Bile Acid as the Stressors
7.2 - O2 and gut microbes
7.2.1 - Response of Obligate Anaerobes to O2 and Reactive Oxygen Species
7.2.2 - Effect of O2 on the Growth of Bifidobacterium
7.2.3 - Enzymes for ROS Detoxification in Bifidobacterium
7.2.4 - Enzymes for H2O2 Production in Bifidobacterium
7.3 - Bile acids as antimicrobials for gut microbes
7.3.1 - Functions of Bile Acids in Humans: Lipid Digestion and Antimicrobial Activity
7.3.2 - Bile Acid Metabolism by Gut Microbes and the Resulting Bile Acid Composition in the Large Intestine
7.3.3 - Antimicrobial Activity of Bile Acids: Mechanism of Action and Structure-Activity Relationship
7.3.4 - Cytotoxicity of SCFAs: Comparison With the Antimicrobial Activity of Bile Acids
7.3.5 - Bile Acids as Host Factors to Control Gut Microbiota Composition
Chapter 8 - Carbohydrate Metabolism in Bifidobacteria
8.2 - Carbohydrate availability in the gastrointesintal tract
8.3 - The bifidobacterial glycobiome
8.4 - The fructose-6-phosphate phosphoketolase pathway
8.5 - Carbohydrate uptake by bifidobacteria
8.6 - Glycosyl hydrolases (GHs) in bifidobacteria
8.7 - Metabolism of plant-derived carbohydrates by bifidobacteria
8.8 - Mucin metabolism by bifidobacteria
8.9 - Metabolism of N-linked glycoproteins
8.10 - Glycosulfatase activity in bifidobacteria
8.11 - Carbohydrate cross-feeding by bifidobacteria
8.12 - Transglycosylation activity in bifidobacteria
8.13 - Regulation of carbohydrate metabolism in bifidobacteria
Chapter 9 - Interactions Between Bifidobacteria, Milk Oligosaccharides, and Neonate Hosts
9.2 - Progression of microbiota in infants
9.4 - Bifidobacterial consumption of milk glycans
9.5 - Nonbifidobacterial HMO consumption
9.6 - Bifidobacterial HMO consumption and colonization of infants
9.7 - Maternal genomic influence on colonization
9.8 - Geographic variation in bifidobacterial colonization
9.9 - Challenges in identification and enumeration of bifidobacteria
9.9.1 - Isolate ID Challenges
9.9.1.1 - Community Analysis of Bifidobacterial Species
Chapter 10 - Biological Activities and Applications of Bifidobacterial Exopolysaccharides: From the Bacteria and Host Perspective
10.1 - Exopolysaccharide synthesis in Bifidobacterium spp.
10.1.1 - Genetic Background
10.1.2 - Hypothetical Biosynthesis Pathway
10.1.3 - Physical–Chemical Composition
10.2 - Biological properties
10.2.1 - Bacterial Protection and Colonization
10.2.2 - Beneficial Effect for the Host
10.2.2.1 - Immune Modulation Capability
10.2.2.2 - Modulators of Intestinal Microbiota
10.2.2.3 - Other Functions
10.3 - Potential applications
10.3.2 - As Prebiotics or Synbiotics
10.4 - Concluding remarks
Chapter 11 - Folate and Bifidobacteria
11.2 - Nomenclature and molecular structure
11.2.1 - Stability and Interconversion
11.3 - Some crucial aspects in measuring bacterial folate production
11.4 - Microbial biosynthesis of folate
11.4.1 - Production of Folate by Bifidobacteria
11.5 - Metabolism and biological function of folate
11.6 - Biotechnology and biofortification
11.6.1 - The Production Organism
11.8 - Concluding remarks
Chapter 12 - Bifidobacteria: Ecology and Coevolution With the Host
12.2 - Ecological origin of bifidobacteria and genetic adaptation to the human gut
12.3 - Genomics of the Bifidobacterium genus
12.4 - How bifidobacterial genomes have been shaped by carbohydrate availability
12.5 - The predicted glycobiomes of bifidobacteria
12.6 - Evaluation of the genetic adaptation of bifidobacteria to the human gut
12.7 - Cross-feeding activities of bifidobacteria
12.8 - Interaction of bifidobacteria with the human gut
12.9 - Concluding remarks
Chapter 13 - Clinical Significance of Bifidobacteria
13.2 - Effects in healthy individuals
13.2.2 - General Health and Prevention of Illness Episodes
13.2.3 - Gastrointestinal Functions
13.2.4 - Immune Activation/Modulation
13.3 - Preterm infants and necrotizing enterocolitis
13.4 - Critically ill patients
13.6.1 - Atopic Dermatitis
13.6.2 - Allergic Rhinitis
13.7 - Inflammatory disorders of the gastrointestinal tract
13.7.2 - Inflammatory Bowel Disease
13.7.3 - Irritable Bowel Syndrome
13.8 - Concluding remarks
Chapter 14 - Honeybee-Specific Bifidobacteria and Lactobacilli
14.4 - The honey stomach microbiota
14.5 - Traditional medicine honey
14.6 - The potential of the honey stomach microbiota: present and future research
14.6.1 - Mechanisms of Action
14.6.3 - Hard-to-Heal Horse Wounds
14.6.4 - Chronic Human Wounds
14.6.5 - Inhibition of Bovine Cow Mastitis Pathogens
14.6.6 - Protection of Honeybees and Their Food
14.6.7 - Future Applications
Chapter 15 - Genetic Manipulation and Gene Modification Technologies in Bifidobacteria
15.2 - Transformation of bifidobacteria
15.2.1 - Escherichia coli–Bifidobacterium Shuttle Vectors
15.2.1.1 - Bifidobacterial Replicons
15.2.1.2 - Antibiotic Resistance Genes
15.2.2 - Electroporation in Bifidobacteria: Issues in Transformation Efficiency and Their Solutions
15.2.3 - Conjugational Transfer System: An Alternative Tool for Transformation
15.3 - Heterologous gene expression in bifidobacteria
15.3.1 - Factors for Regulating Heterologous Gene Expression: Promoters
15.3.2 - Factors for Regulating Heterologous Gene Expression: RBS
15.4 - Gene mutagenesis systems in bifidobacteria
15.4.1 - Targeted Gene Mutagenesis System in Bifidobacteria
15.4.2 - Transposon Mutagenesis System in Bifidobacteria
15.5 - Future perspectives
Chapter 16 - Production of Probiotic Bifidobacteria
Chapter 17 - Prebiotics, Probiotics, and Synbiotics: A Bifidobacterial View
17.2 - Definitions used in scientific research and regulations
17.3 - Clinical effectiveness of probiotics, prebiotics, and synbiotics in otherwise healthy people
17.3.1 - Probiotics, Prebiotics, and Synbiotics in Healthy Infants
17.3.2 - Probiotics, Prebiotics, and Synbiotics in Healthy Adults
17.3.3 - Probiotics, Prebiotics, and Synbiotics in Healthy Elderly People
17.4 - Therapeutic use of probiotics, prebiotics, and synbiotics in gastrointestinal disease
17.5 - Irritable bowel syndrome
17.5.1 - Inflammatory Bowel Disease
17.5.2 - Ulcerative Colitis
17.6 - Necrotic enterocolitis (NEC)
17.7.1 - Diarrheal Diseases
17.7.1.1 - Helicobacter pylori Infection
17.7.2 - Metagenomic Approaches to Assess Mechanisms of Action
Chapter 18 - Evidence of the In Vitro and In Vivo Immunological Relevance of Bifidobacteria
18.2 - In vitro cell models
18.2.1 - Effects on Epithelial Cells
18.2.2 - Effects on Peripheral Blood Mononuclear Cells (PBMCs) and Other Immune Cell Models
18.3 - In vivo animal models
18.3.1 - Effects on Healthy and Gnotobiotic Animal Models
18.3.2 - Effects on Mouse Models of Intestinal Inflammation
18.3.3 - Effects on Pathogen-Infection Models
18.3.4 - Effects on Vaccination
18.3.5 - Effects on Animal Models for Allergic Disease
18.3.6 - Effects on Other Pathologies
18.4 - Mechanisms of interaction with the immune system
18.4.1 - Effect of Compounds Secreted by Bifidobacteria
18.4.2 - Effect of Bifidobacterial Proteins
18.4.3 - Effect of Bifidobacterial Exopolysaccharides
18.4.4 - Effect of Bifidobacterial Metabolites and DNA
18.5 - Concluding remarks
The Bifidobacteria and Related Organisms
：Biology, Taxonomy, Applications
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