1. Methods for the Isolation and Recovery of Bifidobacteria
Abelardo Margolles and Lorena Ruiz
2. Bifidobacterium Transformation
Emily C. Hoedt, Roger S. Bongers, Francesca Bottacini, Jan Knol, John MacSharry, and Douwe van Sinderen
3. Isolation of Chromosomal and Plasmid DNA from Bifidobacteria
Maria Esteban-Torres, Lorena Ruiz, Rocio Sanchez-Gallardo, and Douwe van Sinderen
4. Assembly, Annotation, and Comparative Analysis of Bifidobacterial Genomes
Gabriele Andrea Lugli
5. Site-directed Mutagenesis of Bifidobacterium Strains
Kieran James and Douwe van Sinderen
6. Protocol to Select Bifidobacteria from Fecal and Environmental Samples
Giulia Alessandri, Maria Cristina Ossiprandi, Marco Ventura, and Douwe van Sinderen
7. Phageome Analysis of Bifidobacteria-Rich Samples
Brian McDonnell, Eoghan Casey, Christian Milani, Gabriele Andrea Lugli, Alice Viappiani, Jennifer Mahony, Marco Ventura, and Douwe van Sinderen
8. Measuring Conjugated Linoleic Acid (CLA) Production by Bifidobacteria
Grace Ahern, Douwe van Sinderen, Bo Yang, R. Paul Ross, and Catherine Stanton
9. Detection, Isolation, and Purification of Bifidobacterial Exopolysaccharides
Patricia Ruas Madiedo
10. Determination of Bifidobacterial Carbohydrate Utilisation Abilities and Associated Metabolic End-Products
Ana Solopova and Douwe van Sinderen
11.Model for Murine Gut Colonisation by Bifidobacteria
Valerio Rossini and Ken Nally
12. Identification of Bifidobacteria by the Phosphoketolase Assay
Monica Modesto, Alice Checcucci, and Paola Mattarelli
13. Determination of Bile Salt Hydrolase Activity in Bifidobacteria
Lorena Ruiz, Borja Sanchez, and Abelardo Margolles
14. A Resource for Cloning and Expression Vectors Designed for Bifidobacteria: Overview of Available Tools and Biotechnological Applications
Lorena Ruiz, Maria Esteban-Torres, and Douwe van Sinderen
15. Metagenomic Analyses of Bifidobacterial Communities
Christian Milani
16. Resistance of Bifidobacteria toward Antibiotics
Miguel Gueimonde and Silvia Arboleya
17. In vitro Assessment of Prebiotic Activity
Alberto Amaretti, Stefano Raimondi, Nicola Volpi, and Maddalena Rossi
18. Bifidobacterium Genome Assembly and Methylome Analysis using Pacbio SMRT Sequencing
Francesca Bottacini and Douwe van Sinderen