Bacteriophages, 1st ed. 2024 Methods and Protocols Methods in Molecular Biology Series, Vol. 2738

This volume provides detailed protocols for the isolation, enumeration, characterization of diverse bacteriophages, including both small and jumbo bacteriophages, from soil, fecal, municipal wastewater, and from food niche samples. Chapters highlight the diversity of bacteriophages in different environments, quantifications using culture and molecular techniques, protocols for isolation, interaction of bacteriophage proteins with host cells, and how to use bacteriophages to transfer foreign genetic elements to bacterial strains. In addition to the above, chapters feature the application of bacteriophages/bacteriophage-derived products. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips (in the Notes section) on troubleshooting and avoiding known pitfalls.

Authoritative and cutting-edge, Bacteriophages: Methods and Protocols aims to ensure successful results in further study of this vital field.

PART I       AN OVERVIEW OF THE DIVERSITY OF BACTERIOPHAGES

1.     Structural and genomic diversity of bacteriophages
Bert Ely, Jacob Lenski, Tannaz Mohammadi

3.     Breaking the ice - A review of phages from polar ecosystems
Mara Elena Heinrichs, Goncalo J. Piedade, Ovidiu Popa, Pacifica Sommers, Gareth Trubl, Julia Weissenbach, Janina Rahlff

4.     The diversity of bacteriophages in hot spring
Timothy J. Marks and Isabella R. Rowland   

PART II          ISOLATION OF BACTERIOPHAGES

5.     Isolation of bacteriophage from soil samples in a poorly equipped field lab in Kruger National Park

Ayesha Hassim and Kgaugelo Edward Lekota

6.     Purification and up-concentration of bacteriophages and viruses from fecal samples
Frej Larsen, Rasmus Riemer Jakobsen, Xiaotian Mao, Josue Castro-Mejia, Ling Deng,Dennis S. Nielsen

7.     Isolation of enterococcus phages from municipal wastewater samples using an enrichment step

Cory Schwarz and Jacques Mathieu

8.     Phage DNA extraction, genome assembly, and genome closure

Justin Boeckman, Mei Liu, Jolene Ramsey, and Jason Gill

PART III       ENUMERATION OF BACTERIOPHAGES

9.     Enumeration of bacteriophages by plaque assay

Diana E. Waturangi

10.   Detection and quantification of phages in wastewater samples by culture and molecular methods

Laura Sala-Comorera, Maite Muniesa, and Lorena Rodríguez-Rubio

11.   Flow virometry: A fluorescence-based approach to enumerate bacteriophages in liquid samples

Elena A. Dlusskaya, and Rafik Dey

12.   A metagenomics approach to enumerate bacteriophages in a Food Niche

Kelsey White, Giovanni Eraclio, Gabriele Andrea Lugli, Marco Ventura, Jennifer Mahony, Fabio Dal Bello, and Douwe van Sinderen

PART IV         CHARACTERIZATION OF BACTERIOPHAGES

13.   Bioinformatic analysis of Staphylococcus phages: a key step for safe cocktail development

Soledad Telma Carrasco, and Héctor Ricardo Morbidoni

14.   Use of localized reconstruction to visualize the Shigella-bacteriophage Sf6 tail apparatus

Chun-Feng David Hou, Fenglin Li, Stephano Iglesias, and Gino Cingolani

15.   Bacteriophage-host interactions and co-evolution

Diana Álvarez-Espejo, Dácil Rivera, Andrea I. Moreno-Switt

16.   Unraveling physical interactions of Clostridioides difficile with phage and phage-derived proteins using in vitro and whole-cell assays

17.   Phage Transduction of Staphylococcus aureus

Melissa-Jane Chu Yuan Kee and John Chen

PART V          APPLICATION OF BACTERIOPHAGES AND BACTERIOPHAGE-DERIVED COMPONENTS

18.   The Next Generation of Drug Delivery: Harnessing the Power of Bacteriophages

19.   Construction of nonnatural cysteine-crosslinked phage libraries

 Brittney Chau, Kristi Liivak, Jianmin Gao

20.   Application of next generation sequencing in phage display

 Vincent Van Deuren, Sander Plessers, Rob Lavigne, and Johan Robben

21.   The application of bacteriophage and photoacoustic flow cytometry in bacterial identification

 Robert H. Edgar, Anie-Pier Samson, John A. Viator

22.   Propagation, purification and characterization of bacteriophages for phage

Katarzyna Kosznik-Kwaśnicka, Gracja Topka, Jagoda Mantej, Łukasz Grabowski, Agnieszka Necel, Grzegorz Węgrzyn, Alicja Węgrzyn

23.   Overcoming bacteriophage resistance in phage therapy

Elina Laanto

24.   Bacteriophage virus-like particles: platforms for vaccine design

Ebenezer Tumban

Includes cutting-edge methods and protocols

Provides step-by-step detail essential for reproducible results

Contains key notes and implementation advice from the experts