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.
Highlights
Viral metagenomics has revolutionized the field of virology by providing culture-independent methods to detect and characterize the vast diversity of viruses that cannot be cultured and isolated in a high-throughput manner [1,2,3,4]
Metagenomics is the study of nucleic acid sequences from a collection of entities in a sample, with viral metagenomics focusing on the nucleic acids of viruses within the sample
The array of tools and approaches for viral metagenomics was recently reviewed elsewhere [50, 51], but we summarize key advantages and limitations of cutting-edge techniques within an ecological framework
Summary
Viral metagenomics has revolutionized the field of virology by providing culture-independent methods to detect and characterize the vast diversity of viruses that cannot be cultured and isolated in a high-throughput manner [1,2,3,4]. Metagenomics is the study of nucleic acid sequences from a collection of entities in a sample, with viral metagenomics focusing on the nucleic acids of viruses within the sample. These high-throughput approaches have advanced our understanding of viral ecology by providing insights into the diversity, abundance, and functional potential of viruses associated with different environments [5, 6].
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