Advances in Phage Applications: Deciphering Phage Biological and Ecological Mechanisms through Metagenomics

Phages are ubiquitous particles that infect bacteria and archaea in all environments. In addition to lysing bacteria, phages can also influence bacteria through lysogenic conversion, which can confer immunity to superinfection, and provide expanded metabolic capabilities, such as antibiotic resistance.

For decades, phage discovery and characterization have relied on culture methods for propagation, which depends on a susceptible bacterial host. Microscopy- and PCR-based methods have also enabled the identification and characterization of phages; yet, these methods rely on phage isolation (microscopy), or a priori knowledge of a genomic region of interest (PCR-based methods). For these reasons, agnostic approaches using metagenomics have been applied in phage discovery and characterization for the last 20 years. Phage metagenomics has enabled their characterization in association with human and animal health and disease, and in association with specific environments. It is anticipated that phage discovery, identification and characterization using metagenomics will continue to expand and be applied in diverse fields including, but not limited to phage biology and ecology, as well as phage therapy.

Phage discovery and characterization using viral metagenomics is not without drawbacks. Since known phages may represent < 1% of the microbial component, this hinders the identification and characterization of phages and their potential roles in many environments. Also known as the ‘viral dark matter’, lack of phage homology to current databases may inhibit the taxonomic and functional information obtained. In addition, identification and characterization of phages from metagenomics datasets relies on the bioinformatic tools and databases used. Bioinformatic tools, for instance, are becoming incredibly diverse, some relying on sequence homology and machine learning methods, or a combination of both. Similarly, viral databases have expanded exponentially in the last 4-5 years, demonstrating the importance of utilizing an updated reference database.

In this Research Topic, we will discuss recent advances of high-throughput sequencing applications on, but not limited to, these sub-themes:

- Discovery and characterization of novel phages using currently available and novel bioinformatic tools.

- Identification and characterization of known bacteriophages in association with human and animal health and disease, and the environment.

- Phage ecology through the identification of phage lytic/lysogenic cycles.

- Microbiome changes in association with phage therapy.

We welcome the following manuscript types: Hypothesis & Theory, Methods, Mini Review, Opinion, Original Research, Perspective, Review, Systematic Review, Technology and Code from both experimental and bioinformatic groups addressing the points listed above.

Keywords: metagenomics, microbiome, phage applications, phage therapy

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.