Integrating Viral Metagenomics into an Ecological Framework

Abstract

Viral metagenomics has expanded our knowledge of the ecology of uncultured viruses, within both environmental (e.g., terrestrial and aquatic) and host-associated (e.g., plants and animals, including humans) contexts. Here, we emphasize the implementation of an ecological framework in viral metagenomic studies to address questions in virology rarely considered ecological, which can change our perception of viruses and how they interact with their surroundings. An ecological framework explicitly considers diverse variants of viruses in populations that make up communities of interacting viruses, with ecosystem-level effects. It provides a structure for the study of the diversity, distributions, dynamics, and interactions of viruses with one another, hosts, and the ecosystem, including interactions with abiotic factors. An ecological framework in viral metagenomics stands poised to broadly expand our knowledge in basic and applied virology. We highlight specific fundamental research needs to capitalize on its potential and advance the field. Expected final online publication date for the Annual Review of Virology, Volume 8 is September 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Presence and Persistence of Putative Lytic and Temperate Bacteriophages in Vaginal Metagenomes from South African Adolescents

“…Prophages have previously been identified in BV-associated bacteria [81], yet to our knowledge, we are first to describe full-length bacteriophages that presumably infect BV-associated bacteria. Our untargeted sequencing-based study suggests that virulent bacteriophages targeting BV-associated bacteria are indeed present in the FGT, and determination of near-complete or complete viral genomes such as ours enables a broader understanding of viral evolution and allows classification of these viruses in a rather dynamic taxonomic framework [19,82]. It was somewhat surprising that we were not able to assign taxonomy using vCONTACT 2.…”

“…Local environmental factors may influence the frequencies in which bacteriophages transition from a lysogenic to a lytic life cycle [12][13][14][15]. The switch from lysogeny to a lytic lifecycle of bacteriophages contributes to shaping bacterial communities and favours the dissemination of antibiotic resistance genes and other mobile genetic elements [16][17][18][19]. However, cryptic prophages modulate genetic diversity and functionality of bacterial communities [3,19] and provide fitness benefits to their bacterial host [20][21][22][23][24][25], as well as protection against secondary infection by closely related bacteriophages that belong to the same immunity group [26][27][28].…”

Elevation drives activity of soil bacteria, but not of bacterial viruses

“…The copyright holder for this this version posted December 14, 2021. ; https://doi.org/10.1101/2021.12.14.472558 doi: bioRxiv preprint environment (Sommers et al, 2021). The integration of an ecological framework in viral metagenomics and -transcriptomics could broadly expand our knowledge on ecosystem-level effects of viruses (Roux et al, 2021;Sommers et al, 2021).…”

“…The integration of an ecological framework, such as activity analyses across gradients, into bacteria-virus interaction studies can address questions which have been mostly neglected in virology, but are key to advance our understanding on the ecosystem consequences of predator-prey dynamics (Sommers et al, 2021).…”

“…The aim of this study was to establish a baseline approach to simultaneously assess bacteria and bacteriophage activities and their drivers in soil. To understand community-wide responses to environmental change, in particular to climate, we utilize gradient analyses from an ecological framework (Sommers et al, 2021) to assess the population-wide activities of bacteria and phage communities across an elevational gradient in the European Alps. Elevational gradients allow the study of broad environmental conditions on a condensed geographic scale (Bergner et al, 2020;Neuschulz et al, 2018).…”