Bifidobacteria: Methods and Protocols

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

María Esteban-Torres, Lorena Ruiz, Rocío Sánchez-Gallardo, and Douwe van Sinderen

4. Assembly, Annotation, and Comparative Analysis of Bifidobacterial Genomes

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 Sánchez, and Abelardo Margolles

14. A Resource for Cloning and Expression Vectors Designed for Bifidobacteria: Overview of Available Tools and Biotechnological Applications

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