About this Research Topic

Background

Bacteriophages represent the most abundant biological entities on Earth, but despite large sampling and sequencing efforts, the vast majority of them still remain undiscovered. Characterization of novel
bacteriophages has been hampered by the lack of a universal marker gene, which would serve for detection and classification of phages from environmental samples. As a consequence of this, the databases still do not encompass the whole diversity of bacteriophages on Earth, and there is no universal system for classification of the large number of novel phages that are routinely recovered from metagenomes.

Fortunately, dozens of computational tools addressing the challenges of culture-independent characterization of Earth’s viromes have been developed in the recent years. Thanks to the advances in sequence-based recovery of viral genomes, the number of novel phages is increasing exponentially, which allows us to study how bacteriophages influence biological aspects across all environments, including water, soil, extreme ecosystems or host-associated microbiomes, and even human health. The current tools for detection, functional annotation, and classification of phages from environmental samples involve different computational approaches. The performance of these tools is influenced by a variety of factors, such as different training sets of samples used for their development, different reference sequence databases, or different stringency in dealing with the host sequence contamination. The field of viromics is evolving rapidly, and with the increasing number of novel types of phages, new challenges are emerging.

In this Research Topic, we call for original research manuscripts describing viromes from all environments, including soil, terrestrial, marine, and host-associated microbiomes. We encourage the
use of multiple computational tools for bacteriophage detection, classification, or characterization, or testing different parameters of the same tool. Manuscripts describing new computational tools or
identifying new challenges in viromics are welcome.

Please note that Phage Biology does not consider descriptive studies that are solely based on amplicon profiles, unless they are accompanied by a clear hypothesis and experimentation and provide
insight into the microbiological system or process being studied. If your manuscript include amplicon profiles please make sure that your abstract include a clear statement on why we should consider your
manuscript. Please, specify in your abstract the methods used to test the hypothesis and how the reported results support and validate this hypothesis.

Keywords: phages, bioinformatics, viromes, metagenomics, uncultured microbes, environmental microbiology, human microbiome

Important note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.

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