CheckV assesses the quality and completeness of metagenome-assembled viral genomes

Nature Biotechnology, Journal Year: 2020, Volume and Issue: 39(5), P. 578 - 585

Published: Dec. 21, 2020

Abstract Millions of new viral sequences have been identified from metagenomes, but the quality and completeness these vary considerably. Here we present CheckV, an automated pipeline for identifying closed genomes, estimating genome fragments removing flanking host regions integrated proviruses. CheckV estimates by comparing with a large database complete including 76,262 systematic search publicly available metatranscriptomes metaviromes. After validation on mock datasets comparison to existing methods, applied diverse collections metagenome-assembled sequences, IMG/VR Global Ocean Virome. This revealed 44,652 high-quality genomes (that is, >90% complete), although vast majority were small fragments, which highlights challenge assembling short-read metagenomes. Additionally, found that removal contamination substantially improved accurate identification auxiliary metabolic genes interpretation viral-encoded functions.

Language: Английский

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VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses

Microbiome, Journal Year: 2021, Volume and Issue: 9(1)

Published: Feb. 1, 2021

Viruses are a significant player in many biosphere and human ecosystems, but most signals remain "hidden" metagenomic/metatranscriptomic sequence datasets due to the lack of universal gene markers, database representatives, insufficiently advanced identification tools.Here, we introduce VirSorter2, DNA RNA virus tool that leverages genome-informed advances across collection customized automatic classifiers improve accuracy range detection. When benchmarked against genomes from both isolated uncultivated viruses, VirSorter2 uniquely performed consistently with high (F1-score > 0.8) viral diversity, while all other tools under-detected viruses outside group represented reference databases (i.e., those order Caudovirales). Among evaluated, was also able minimize errors associated atypical cellular sequences including eukaryotic plasmids. Finally, as virosphere exploration unravels novel sequences, VirSorter2's modular design makes it inherently expand new types via maintain maximal sensitivity specificity.With multi-classifier design, demonstrates higher overall major groups will advance our knowledge evolution, virus-microbe interaction various ecosystems. Source code is freely available ( https://bitbucket.org/MAVERICLab/virsorter2 ), on bioconda an iVirus app CyVerse https://de.cyverse.org/de ). Video abstract.

Language: Английский

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Phage diversity, genomics and phylogeny

Nature Reviews Microbiology, Journal Year: 2020, Volume and Issue: 18(3), P. 125 - 138

Published: Feb. 3, 2020

Language: Английский

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The Human Gut Virome Is Highly Diverse, Stable, and Individual Specific

Cell Host & Microbe, Journal Year: 2019, Volume and Issue: 26(4), P. 527 - 541.e5

Published: Oct. 1, 2019

Language: Английский

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Minimum Information about an Uncultivated Virus Genome (MIUViG)

Nature Biotechnology, Journal Year: 2018, Volume and Issue: 37(1), P. 29 - 37

Published: Dec. 17, 2018

This paper presents standards and best practices for reporting genome sequences of uncultivated viruses. We present an extension the Minimum Information about any (x) Sequence (MIxS) standard virus genomes. Uncultivated Virus Genome (MIUViG) were developed within Genomic Standards Consortium framework include origin, quality, annotation, taxonomic classification, biogeographic distribution in silico host prediction. Community-wide adoption MIUViG standards, which complement a Single Amplified (MISAG) Metagenome-Assembled (MIMAG) bacteria archaea, will improve genomes public databases. In turn, this should enable more robust comparative studies systematic exploration global virosphere.

Language: Английский

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Massive expansion of human gut bacteriophage diversity

Cell, Journal Year: 2021, Volume and Issue: 184(4), P. 1098 - 1109.e9

Published: Feb. 1, 2021

Bacteriophages drive evolutionary change in bacterial communities by creating gene flow networks that fuel ecological adaptions. However, the extent of viral diversity and its prevalence human gut remains largely unknown. Here, we introduce Gut Phage Database, a collection ∼142,000 non-redundant genomes (>10 kb) obtained mining dataset 28,060 globally distributed metagenomes 2,898 reference cultured bacteria. Host assignment revealed is highest Firmicutes phyla ∼36% clusters (VCs) are not restricted to single species, across phylogenetically distinct species. Epidemiological analysis uncovered 280 VCs found at least 5 continents highly prevalent phage clade with features reminiscent p-crAssphage. This high-quality, large-scale catalog will improve future virome studies enable bacteriophages.

Language: Английский

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Clades of huge phages from across Earth’s ecosystems

Nature, Journal Year: 2020, Volume and Issue: 578(7795), P. 425 - 431

Published: Feb. 12, 2020

Bacteriophages typically have small genomes

Language: Английский

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Interactions between bacterial and phage communities in natural environments

Nature Reviews Microbiology, Journal Year: 2021, Volume and Issue: 20(1), P. 49 - 62

Published: Aug. 9, 2021

Language: Английский

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Whole-Virome Analysis Sheds Light on Viral Dark Matter in Inflammatory Bowel Disease

Cell Host & Microbe, Journal Year: 2019, Volume and Issue: 26(6), P. 764 - 778.e5

Published: Nov. 19, 2019

Language: Английский

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IMG/VR v3: an integrated ecological and evolutionary framework for interrogating genomes of uncultivated viruses

Nucleic Acids Research, Journal Year: 2020, Volume and Issue: 49(D1), P. D764 - D775

Published: Oct. 9, 2020

Viruses are integral components of all ecosystems and microbiomes on Earth. Through pervasive infections their cellular hosts, viruses can reshape microbial community structure drive global nutrient cycling. Over the past decade, viral sequences identified from genomes metagenomes have provided an unprecedented view genome diversity in nature. Since 2016, IMG/VR database has access to largest collection obtained (meta)genomes. Here, we present third version IMG/VR, composed 18 373 cultivated 2 314 329 uncultivated (UViGs), nearly tripling total number compared previous version. These clustered into 935 362 Operational Taxonomic Units (vOTUs), including 188 930 with two or more members. UViGs now reported as single contigs, integrated proviruses bins, annotated a new standardized pipeline quality estimation using CheckV, taxonomic classification reflecting latest ICTV update, expanded host taxonomy prediction. The interface enables users efficiently browse, search, select based features and/or sequence similarity. v3 is available at https://img.jgi.doe.gov/vr, underlying data download https://genome.jgi.doe.gov/portal/IMG_VR.

Language: Английский

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