TY - CHAP

T1 - Purification and Up-Concentration of Bacteriophages and Viruses from Fecal Samples

AU - Larsen, Frej

AU - Jakobsen, Rasmus Riemer

AU - Mao, Xiaotian

AU - Castro-Mejia, Josue

AU - Deng, Ling

AU - Nielsen, Dennis S.

N1 - Publisher Copyright: © The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature 2024.

PY - 2024

Y1 - 2024

N2 - The viral fraction of human and experimental animal fecal matter is increasingly attracting research interest due to its newfound influence on the gut microbiome and host health. During the past decade, high-throughput sequencing techniques have seen massive improvements, and in recent years, bioinformatics pipelines for virome analysis have also vastly improved with respect to both user-friendliness and output quality. Yet, the shape and quality of such data are highly dependent on how the viruses are isolated and their genomes extracted and processed to build sequencing libraries. Here we describe a simple protocol for virus isolation from fecal samples suitable for further propagation/characterization or sequencing efforts. It is based on two filtration steps: one for removing large particles such as bacteria and one for removing free DNA and up-concentrating phages and other viruses in the solution. The method is highly scalable, adaptable to a long range of sample types including low-input samples, and has a quantifiable output suitable for both plaquing and sequencing.

AB - The viral fraction of human and experimental animal fecal matter is increasingly attracting research interest due to its newfound influence on the gut microbiome and host health. During the past decade, high-throughput sequencing techniques have seen massive improvements, and in recent years, bioinformatics pipelines for virome analysis have also vastly improved with respect to both user-friendliness and output quality. Yet, the shape and quality of such data are highly dependent on how the viruses are isolated and their genomes extracted and processed to build sequencing libraries. Here we describe a simple protocol for virus isolation from fecal samples suitable for further propagation/characterization or sequencing efforts. It is based on two filtration steps: one for removing large particles such as bacteria and one for removing free DNA and up-concentrating phages and other viruses in the solution. The method is highly scalable, adaptable to a long range of sample types including low-input samples, and has a quantifiable output suitable for both plaquing and sequencing.

KW - Bacteriophages

KW - Fecal virome

KW - Ultrafiltration

KW - Virus purification

KW - Viruses

KW - VLP extraction

U2 - 10.1007/978-1-0716-3549-0_6

DO - 10.1007/978-1-0716-3549-0_6

M3 - Book chapter

C2 - 37966594

AN - SCOPUS:85177102912

T3 - Methods in Molecular Biology

SP - 105

EP - 110

BT - Bacteriophages

PB - Humana Press

ER -