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

Nature Biotechnology, Год журнала: 2020, Номер 39(5), С. 578 - 585

Опубликована: Дек. 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.

Язык: Английский

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

Microbiome, Год журнала: 2021, Номер 9(1)

Опубликована: Фев. 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.

Язык: Английский

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Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks

Nature Biotechnology, Год журнала: 2019, Номер 37(6), С. 632 - 639

Опубликована: Май 6, 2019

Язык: Английский

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VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences

Microbiome, Год журнала: 2020, Номер 8(1)

Опубликована: Июнь 10, 2020

Viruses are central to microbial community structure in all environments. The ability generate large metagenomic assemblies of mixed and viral sequences provides the opportunity tease apart complex microbiome dynamics, but these analyses currently limited by tools available for genomes assessing their metabolic impacts on microbiomes.Here we present VIBRANT, first method utilize a hybrid machine learning protein similarity approach that is not reliant sequence features automated recovery annotation viruses, determination genome quality completeness, characterization function from assemblies. VIBRANT uses neural networks signatures newly developed v-score metric circumvents traditional boundaries maximize identification lytic integrated proviruses, including highly diverse viruses. highlights auxiliary genes pathways, thereby serving as user-friendly platform evaluating function. was trained validated reference virus datasets well virome data.VIBRANT showed superior performance recovering higher viruses concurrently reduced false non-viral fragments comparison other programs, specifically VirSorter, VirFinder, MARVEL. When applied 120,834 metagenome-derived representing several human natural environments, recovered an average 94% whereas MARVEL achieved less powerful performance, averaging 48%, 87%, 71%, respectively. Similarly, identified more total proteins when real metagenomes. compared PHASTER, Prophage Hunter, VirSorter extract provirus regions host scaffolds, performed comparably even proviruses programs did not. To demonstrate applications studied viromes associated with Crohn's disease show specific groups, namely Enterobacteriales-like putative dysbiosis abundant healthy individuals, providing possible link maintenance diseased states.The accurately recover explore metabolism will greatly advance our understanding microbiomes, host-microbe interactions, ecosystem dynamics. Video Abstract.

Язык: Английский

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Marine DNA Viral Macro- and Microdiversity from Pole to Pole

Cell, Год журнала: 2019, Номер 177(5), С. 1109 - 1123.e14

Опубликована: Апрель 25, 2019

Язык: Английский

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DRAM for distilling microbial metabolism to automate the curation of microbiome function

Nucleic Acids Research, Год журнала: 2020, Номер 48(16), С. 8883 - 8900

Опубликована: Июль 22, 2020

Abstract Microbial and viral communities transform the chemistry of Earth's ecosystems, yet specific reactions catalyzed by these biological engines are hard to decode due absence a scalable, metabolically resolved, annotation software. Here, we present DRAM (Distilled Refined Annotation Metabolism), framework translate deluge microbiome-based genomic information into catalog microbial traits. To demonstrate applicability across diverse genomes, evaluated performance on defined, in silico soil community previously published human gut metagenomes. We show that accurately assigned contributions geochemical cycles automated partitioning carbohydrate metabolism at substrate levels. DRAM-v, mode DRAM, established rules identify virally-encoded auxiliary metabolic genes (AMGs), resulting categorization thousands putative AMGs from soils guts. Together DRAM-v provide critical profiling capabilities decipher mechanisms underpinning microbiome function.

Язык: Английский

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A practical guide to amplicon and metagenomic analysis of microbiome data

Protein & Cell, Год журнала: 2020, Номер 12(5), С. 315 - 330

Опубликована: Май 11, 2020

Abstract Advances in high-throughput sequencing (HTS) have fostered rapid developments the field of microbiome research, and massive datasets are now being generated. However, diversity software tools complexity analysis pipelines make it difficult to access this field. Here, we systematically summarize advantages limitations methods. Then, recommend specific for amplicon metagenomic analyses, describe commonly-used databases, help researchers select appropriate tools. Furthermore, introduce statistical visualization methods suitable analysis, including alpha- beta-diversity, taxonomic composition, difference comparisons, correlation, networks, machine learning, evolution, source tracing, common styles informed choices. Finally, a step-by-step reproducible guide is introduced. We hope review will allow carry out data more effectively quickly order efficiently mine biological significance behind data.

Язык: Английский

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The Gut Virome Database Reveals Age-Dependent Patterns of Virome Diversity in the Human Gut

Cell Host & Microbe, Год журнала: 2020, Номер 28(5), С. 724 - 740.e8

Опубликована: Авг. 24, 2020

Язык: Английский

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Massive expansion of human gut bacteriophage diversity

Cell, Год журнала: 2021, Номер 184(4), С. 1098 - 1109.e9

Опубликована: Фев. 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.

Язык: Английский

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A Roadmap for Genome-Based Phage Taxonomy

Viruses, Год журнала: 2021, Номер 13(3), С. 506 - 506

Опубликована: Март 18, 2021

Bacteriophage (phage) taxonomy has been in flux since its inception over four decades ago. Genome sequencing put pressure on the classification system and recent years have seen significant changes to phage taxonomy. Here, we reflect state of provide a roadmap for future, including abolition order Caudovirales families Myoviridae, Podoviridae, Siphoviridae. Furthermore, specify guidelines demarcation species, genus, subfamily family-level ranks tailed

Язык: Английский

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