Daily Reports on Phage-Host Interactions

Abstract

Understanding phage-host relationships is crucial for the study of virus biology and the application of phages in biotechnology and medicine. However, information concerning the range of hosts for bacterial and archaeal viruses is scattered across numerous databases and is difficult to obtain. Therefore, here we present PHD (Phage & Host Daily), a web application that offers a comprehensive, up-to-date catalog of known phage-host associations that allows users to select viruses targeting specific bacterial and archaeal taxa of interest. Our service combines the latest information on virus-host interactions from seven source databases with current taxonomic classification retrieved directly from the groups and institutions responsible for its maintenance. The web application also provides summary statistics on host and virus diversity, their pairwise interactions, and the host range of deposited phages. PHD is updated daily and available at http://phdaily.info or http://combio.pl/phdaily.

Keywords: archaea; bacteria; database; host; phage; phage-host interactions; web application.

FIGURE 1

Genomic and taxonomic diversity of prokaryotic viruses and their hosts (as of May 1, 2022). (A) Number of different virus taxonomic units across six taxonomic ranks (from species to phylum) according to National Center for Biotechnology Information (NCBI) Taxonomy and the International Committee on Taxonomy of Viruses (ICTV). (B) Ten most abundant virus families represented by the highest number of virus species. (C,D) The number of representative viral genomes stratified by genome composition and assembly level. (E) Size distribution of completely sequenced virus genomes. The red vertical line indicates the median genome size, and the light gray background represents the range between the 5^th and 95^th percentiles. (F) Proportion of viruses isolated on the top 15 most abundant host genera (i.e., host genera infected by the highest number of viruses). (G) Number of different taxonomic units of bacterial and archaeal hosts across seven taxonomic ranks compared to the number of all bacterial and archaeal taxa present in NCBI Assembly. (H) Ten most abundant host classes represented by the highest number of known host species. (I) Number of virus species isolated on a different number of host species. (J) Comparison of the number of pairwise interactions between virus and host species in different databases. (K) Unique and shared virus-host interactions among four databases. The bar chart indicates the intersection size of virus-host interactions. Connected black dots on the bottom panel indicate which combination of the databases was considered for each intersection. Single, unconnected black dots represent virus-host interactions unique to each database (L) Number of genomes and virus species reported daily in the last 2 months (from March 1 to May 1, 2022). Virus genomes were assigned to species based on the then-most-recent NCBI Taxonomy.