MVP: a microbe–phage interaction database

Abstract

Phages invade microbes, accomplish host lysis and are of vital importance in shaping the community structure of environmental microbiota. More importantly, most phages have very specific hosts; they are thus ideal tools to manipulate environmental microbiota at species-resolution. The main purpose of MVP (Microbe Versus Phage) is to provide a comprehensive catalog of phage–microbe interactions and assist users to select phage(s) that can target (and potentially to manipulate) specific microbes of interest. We first collected 50 782 viral sequences from various sources and clustered them into 33 097 unique viral clusters based on sequence similarity. We then identified 26 572 interactions between 18 608 viral clusters and 9245 prokaryotes (i.e. bacteria and archaea); we established these interactions based on 30 321 evidence entries that we collected from published datasets, public databases and re-analysis of genomic and metagenomic sequences. Based on these interactions, we calculated the host range for each of the phage clusters and accordingly grouped them into subgroups such as ‘species-’, ‘genus-’ and ‘family-’ specific phage clusters. MVP is equipped with a modern, responsive and intuitive interface, and is freely available at: http://mvp.medgenius.info.

ACI‐1 beta‐lactamase is widespread across human gut microbiomes in Negativicutes due to transposons harboured by tailed prophages

“…Cross-species phage infection would be required to explain the phylogenetic distribution of aci1 we observed. However, phages generally have a narrow host range limited to a species, sometimes even strains within a species (Gao et al, 2018). Yet examples of polyvalent transgenus infecting phages are increasingly described for the Actinobacteria and Proteobacteria phyla (Petrovski et al, 2011;Hamdi et al, 2017;Kauffman et al, 2018), and cross-species infecting phages are also known for classical Firmicutes (El Haddad et al, 2014), but nothing is known for the Negativicutes.…”

The virome in adult monozygotic twins with concordant or discordant gut microbiomes

“…220 There were no significant differences between groups for any taxa at the Order and 221 Family levels, including crAssphage and Microviridae families ( Figure 4B). 222 We used CRISPR spacer mapping and the microbe-versus-phage (MVP) 223 database (Gao et al, 2018) to predict hosts for virotypes and taxonomically 224 characterized contigs (See Methods). As host annotation was directed to 225 bacteriophages, we did not gain any information for contigs annotated as Eukaryotic 226 viruses.…”

Comparative genomics groups phages of Negativicutes and classical Firmicutes despite different Gram‐staining properties

“…This close relationship between Veillonellales and Acidaminococcales prophages might not necessarily reflect close evolutionary relationships of the bacterial hosts but could instead be the result from cross‐order phage infection. With laboratory‐adapted phages, infections across genus borders are rare and sequence homology analyses generally support this (Gao et al ., ), but microbial ecologists have recently provided data suggesting that phage infections across larger taxonomic borders occur in the natural environment at much higher frequency than anticipated from laboratory experiments (Kauffman et al ., ).…”

“…When the dots are highly dense a solid block of colour shows a larger group of sequence-related prophages infecting the same bacterial host. generally support this (Gao et al, 2017), but microbial ecologists have recently provided data suggesting that phage infections across larger taxonomic borders occur in the natural environment at much higher frequency than anticipated from laboratory experiments (Kauffman et al, 2018).…”