Genome Sequences of Microviruses Identified in Gila Monster Feces

Abstract

The complete genome sequences of 33 microviruses were determined from fecal samples collected from 14 Arizona-dwelling Gila monsters using high-throughput sequencing. These microviruses with genomes 4,383 to 6,782 nucleotides (nt) long were broadly distributed across the 14 samples.

Organizing the Global Diversity of Microviruses

“…We further investigated microvirus sequences from recent large-scale catalogs of human gut phages—the Cenote Human Virome Database ( 3 ) and the Metagenomic Gut Virus Database ( 28 )—as well as microviruses from a global ocean virome data set ( 29 ) and three additional data sets from recent microvirus-related publications ( 30 – 32 ). Together with the aforementioned wastewater data set, we amassed 9,198 new microvirus genomes, more than twice the number of our original genomes ( Table S3 ).…”

“…New alignments of VP1 proteins and subsequent HMM searches were performed iteratively with the inclusion of new sequences until no new microviruses could be detected. Using the final set of HMMs from our curated database, searches for microviruses were conducted on the wastewater data set of Kirstahler et al ( 27 ), the Cenote Human Virome Database ( 3 ), the Metagenomic Gut Virus Database ( 28 ), a global ocean virome data set of Gregory et al ( 29 ), and three additional data sets from recent microvirus-related publications ( 30 – 32 ), all of which had previously undergone gene calling using PHANOTATE. Contigs containing microvirus hits were extracted and directly (i.e., without further annotation or curation for quality and completeness) used as input for MOP-UP.…”

New Microviridae isolated from Sulfitobacter reveals two cosmopolitan subfamilies of ssDNA phages infecting marine and terrestrial Alphaproteobacteria

“…The second cluster was larger, with 21 new prophages and two episomes, 30 EVGs, and three recent isolated phages infecting Rhizobium (van Cauwenberghe et al 2021). All the EVGs here were previously identified as Microviridae in different viromics studies (see SI file 6) ( Creasy et al 2018; Orton et al 2020; Tisza et al 2020; Collins et al 2021) . In two of the studies, the respective EVGs were recognized already to represent a separate group from the known Microviridae subfamilies (Creasy et al 2018; Orton et al 2020).…”

“…4, SI file 4, Table 2, and SI file 6). We found occultatumvirus EVGs in viromes from the lizard Heloderma suspectum (Collins et al 2021), the fishes Carassius carassius, Lutjanus campechanus and Pimephales sp., the snail Haliotis sp . (Tisza et al 2020), the tortoise Gopherus morafkai (Orton et al 2020) and the sea squirt Ciona robusta (Creasy et al 2018).…”

Genome Sequences of Microviruses Identified in a Sample from a Sewage Treatment Oxidation Pond

“…Microviridae is a family of singled-stranded DNA viruses with circular genomes ( 17 ) that have been identified in a broad range of samples types and environments ( 18 – 31 ), including sewage ( 3 , 32 , 33 ). Two subfamilies have been established in the family, namely, Bullavirinae and Gokushovirinae .…”