Freshwater Viromes: From Sampling to Evaluation

Catherine Putonti; Zoë Diener; Siobhan C Watkins

doi:10.1007/978-1-4939-8728-3_2

Freshwater Viromes: From Sampling to Evaluation

Methods Mol Biol. 2018:1849:17-27. doi: 10.1007/978-1-4939-8728-3_2.

Authors

Catherine Putonti^{1

2

3

4}, Zoë Diener⁵, Siobhan C Watkins⁶

Affiliations

¹ Department of Biology, Loyola University Chicago, Chicago, IL, USA.
² Department of Computer Science, Loyola University Chicago, Chicago, IL, USA.
³ Bioinformatics Program, Loyola University Chicago, Chicago, IL, USA.
⁴ Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA.
⁵ Department of Biology, New Mexico Institute for Mining and Technology, Socorro, NM, USA.
⁶ Department of Biology, New Mexico Institute for Mining and Technology, Socorro, NM, USA. swatkins@nmt.edu.

PMID: 30298245
DOI: 10.1007/978-1-4939-8728-3_2

Abstract

There are a number of options available to researchers who wish to collect and analyze viral metagenomes (viromes) from environmental samples. Here we describe a laboratory procedure for generation of viromes from freshwater samples, specifically targeting dsDNA bacteriophages. We also discuss methods for bioinformatic analysis of the resulting data.

Keywords: Bacteriophage; Freshwater viruses; Metagenomics; Viral bioinformatics; Viromes.

Publication types

Evaluation Study
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Bacteriophages / genetics*
Computational Biology
Environmental Monitoring / methods*
Fresh Water / virology*
Genome, Viral*
Metagenomics / methods*
Phylogeny