title: Freshwater Metaviromics and Bacteriophages: A Current Assessment of the State of the Art in Relation to Bioinformatic Challenges.
abstract: Advances in bioinformatics and sequencing technologies have allowed for the analysis of complex microbial communities at an unprecedented rate. While much focus is often placed on the cellular members of these communities, viruses play a pivotal role, particularly bacteria-infecting viruses (bacteriophages); phages mediate global biogeochemical processes and drive microbial evolution through bacterial grazing and horizontal gene transfer. Despite their importance and ubiquity in nature, very little is known about the diversity and structure of viral communities. Though the need for culture-based methods for viral identification has been somewhat circumvented through metagenomic techniques, the analysis of metaviromic data is marred with many unique issues. In this review, we examine the current bioinformatic approaches for metavirome analyses and the inherent challenges facing the field as illustrated by the ongoing efforts in the exploration of freshwater phage populations.
authors.affiliation: Department of Biology, Loyola University Chicago, Chicago, IL, USA.
authors.forename: Katherine
authors.initials: K
authors.lastname: Bruder
authors.affiliation: Department of Biology, Loyola University Chicago, Chicago, IL, USA.
authors.forename: Kema
authors.initials: K
authors.lastname: Malki
authors.affiliation: Department of Biology, Loyola University Chicago, Chicago, IL, USA.
authors.forename: Alexandria
authors.initials: A
authors.lastname: Cooper
authors.affiliation: Department of Biology, Loyola University Chicago, Chicago, IL, USA.
authors.forename: Emily
authors.initials: E
authors.lastname: Sible
authors.affiliation: Department of Biology, Loyola University Chicago, Chicago, IL, USA.; Bioinformatics Program, Loyola University Chicago, Chicago, IL, USA.
authors.forename: Jason W
authors.initials: JW
authors.lastname: Shapiro
authors.affiliation: Department of Biology, Loyola University Chicago, Chicago, IL, USA.
authors.forename: Siobhan C
authors.initials: SC
authors.lastname: Watkins
authors.affiliation: Department of Biology, Loyola University Chicago, Chicago, IL, USA.; Bioinformatics Program, Loyola University Chicago, Chicago, IL, USA.; Department of Computer Science, Loyola University Chicago, Chicago, IL, USA.
authors.forename: Catherine
authors.initials: C
authors.lastname: Putonti
keywords: bacteriophages; environmental metagenomics; freshwater; metaviromics