Microviruses: A World Beyond phiX174

Abstract

Two decades of metagenomic analyses have revealed that in many environments, small (∼5 kb), single-stranded DNA phages of the family Microviridae dominate the virome. Although the emblematic microvirus phiX174 is ubiquitous in the laboratory, most other microviruses, particularly those of the gokushovirus and amoyvirus lineages, have proven to be much more elusive. This puzzling lack of representative isolates has hindered insights into microviral biology. Furthermore, the idiosyncratic size and nature of their genomes have resulted in considerable misjudgments of their actual abundance in nature. Fortunately, recent successes in microvirus isolation and improved metagenomic methodologies can now provide us with more accurate appraisals of their abundance, their hosts, and their interactions. The emerging picture is that phiX174 and its relatives are rather rare and atypical microviruses, and that a tremendous diversity of other microviruses is ready for exploration.

Metagenomic survey of viral diversity obtained from feces of piglets with diarrhea

“…Bacteriophage virus also accounted for a large proportion of the feces of diarrheic piglets, which mainly consisted of the Microvirade and Caudovirales . As one of the most common ssDNA phage viruses, the family Microviridae are small, circular, single-stranded DNA viruses [ 46 ]. A phylogenetic analysis was performed using the amino acid sequence of the major capsid protein (MCP) of the 396 Microviridae strains ( Fig.…”

A stargate mechanism ofMicroviridaegenome delivery unveiled by cryogenic electron tomography

“…However, sequence alignment with WGS genome entries of Rhodobacter strains, confirms that Ebor is transiently integrated as a prophage within the RuBisCO cbbII operon of R. capsulatus DE442, at the same site used by the dsDNA membrane-containing prophage Jorvik (3). Like in Microviridae and other ssDNA prophages, it is flanked by XerCD-binding dif motifs (14,25) ( Figure 1b ). The prophage was also detected in chromosome contigs of DE442-related strains Y262 and R121 (26) but is absent from the parental strain SB1003, and its precursor, the wild-type strain B10 (27).…”

“…The capsids shelter a circular ssDNA genome with sizes potentially ranging from 3.0 kb to 8.9 kb as suggested by metagenomic sequences (12,13). The genome usually encodes 6 to 10 proteins among which the major capsid protein VP1/F, DNA pilot protein VP2/H, internal scaffolding protein VP3/B, genome replication initiation protein VP4/A, and the ssDNA-binding protein VP8/J (14), stand out as most common.…”

Determinants in the phage life cycle: The dynamic nature of ssDNA phage FLiP and host interactions under varying environmental conditions and growth phases

“…FLiP represents a minority in phage studies in at least three fundamental ways as it is tailless, lipid-containing and has a ssDNA genome. Although ssDNA viruses are important players in the aquatic ecosystem (Brum et al, 2013;Holmfeldt et al, 2013;Kauffman et al, 2018;Kirchberger et al, 2022;Kirchberger & Ochman, 2023;Van Cauwenberghe et al, 2022), the empirical studies concerning ssDNA phages have been overshadowed by studies done with dsDNA phages. Furthermore, FLiP infects flavobacteria, which form one of the most prevalent groups of environmental bacteria (Bartlau et al, 2022;Eiler & Bertilsson, 2004, 2007 indicating the possibility of a large ecological impact of FLiP and its relatives.…”