Organochlorine contamination enriches virus-encoded metabolism and pesticide degradation associated auxiliary genes in soil microbiomes DOI Creative Commons
Xiaoxuan Zheng, Martin T. Jahn, Mingming Sun

et al.

The ISME Journal, Journal Year: 2022, Volume and Issue: 16(5), P. 1397 - 1408

Published: Jan. 17, 2022

Viruses significantly influence local and global biogeochemical cycles help bacteria to survive in different environments by encoding various auxiliary metabolic genes (AMGs) associated with energy acquisition, stress tolerance degradation of xenobiotics. Here we studied whether bacterial (dsDNA) virus encoded AMGs are enriched organochlorine pesticide (OCP) contaminated soil China if viral include linked OCP biodegradation. Using metagenomics, found that OCP-contaminated soils displayed a lower bacterial, but higher diversity viruses harbored relative abundance metabolism. Furthermore, the increased along severity contamination, several biodegradation were identified bioinformatically metagenomes. Functional assays conducted experimentally demonstrate virus-encoded L-2-haloacid dehalogenase gene (L-DEX) is responsible for precursors, improving growth at sub-inhibitory concentrations. Taken together, these results metabolism biodegradation, being more abundant diverse pesticides. Moreover, our findings highlight importance accessory ecology stressful environments, providing novel avenue using bioremediation soils.

Language: Английский

Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants DOI
Kira S. Makarova, Yuri I. Wolf, Jaime Iranzo

et al.

Nature Reviews Microbiology, Journal Year: 2019, Volume and Issue: 18(2), P. 67 - 83

Published: Dec. 19, 2019

Language: Английский

Citations

1951
CheckV assesses the quality and completeness of metagenome-assembled viral genomes DOI Creative Commons
Stephen Nayfach, Antônio Pedro Camargo, Frederik Schulz

et al.

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

Citations

1044
DRAM for distilling microbial metabolism to automate the curation of microbiome function DOI
Michael Shaffer, Mikayla Borton, Bridget McGivern

et al.

Nucleic Acids Research, Journal Year: 2020, Volume and Issue: 48(16), P. 8883 - 8900

Published: July 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.

Language: Английский

Citations

732
Global Organization and Proposed Megataxonomy of the Virus World DOI Open Access
Eugene V. Koonin, Valerian V. Dolja, Mart Krupovìč

et al.

Microbiology and Molecular Biology Reviews, Journal Year: 2020, Volume and Issue: 84(2)

Published: March 3, 2020

Viruses and mobile genetic elements are molecular parasites or symbionts that coevolve with nearly all forms of cellular life. The route virus replication protein expression is determined by the viral genome type. Comparison these routes led to classification viruses into seven “Baltimore classes” (BCs) define major features reproduction. However, recent phylogenomic studies identified multiple evolutionary connections among within each BCs as well between different classes.

Language: Английский

Citations

531
Massive expansion of human gut bacteriophage diversity DOI Creative Commons

Luis F. Camarillo-Guerrero,

Alexandre Almeida, Guillermo Rangel-Piñeros

et al.

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

Citations

471
CRISPR-CasΦ from huge phages is a hypercompact genome editor DOI
Patrick Pausch, Basem Al-Shayeb, Ezra Bisom-Rapp

et al.

Science, Journal Year: 2020, Volume and Issue: 369(6501), P. 333 - 337

Published: July 17, 2020

Compact defense system in bacteriophages The CRISPR-Cas system, naturally found many prokaryotes, is widely used for genome editing. CRISPR arrays the bacterial genome, derived from of invading viruses, are to generate a RNA that guides Cas enzyme destroy repeat viral invaders. Recently, an unexpectedly compact was identified huge bacteriophages. Pausch et al . show even though this lacks commonly accessory proteins, it functional. In addition array, only component called CasF, which uses same active site process transcripts into and foreign nucleic acids. This human plant cells, provides hypercompact genome-editing toolbox. Science issue p. 333

Language: Английский

Citations

443
A Roadmap for Genome-Based Phage Taxonomy DOI Creative Commons
Dann Turner, Andrew M. Kropinski, Evelien M. Adriaenssens

et al.

Viruses, Journal Year: 2021, Volume and Issue: 13(3), P. 506 - 506

Published: March 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

Language: Английский

Citations

418
Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome DOI Creative Commons
Stephen Nayfach, David Páez-Espino, Lee Call

et al.

Nature Microbiology, Journal Year: 2021, Volume and Issue: 6(7), P. 960 - 970

Published: June 24, 2021

Bacteriophages have important roles in the ecology of human gut microbiome but are under-represented reference databases. To address this problem, we assembled Metagenomic Gut Virus catalogue that comprises 189,680 viral genomes from 11,810 publicly available stool metagenomes. Over 75% represent double-stranded DNA phages infect members Bacteroidia and Clostridia classes. Based on sequence clustering identified 54,118 candidate species, 92% which were not found existing The improves detection viruses metagenomes accounts for nearly 40% CRISPR spacers Bacteria Archaea. We also produced a 459,375 protein clusters to explore functional potential virome. This revealed tens thousands diversity-generating retroelements, use error-prone reverse transcription mutate target genes may be involved molecular arms race between their bacterial hosts.

Language: Английский

Citations

408
Petabase-scale sequence alignment catalyses viral discovery DOI Creative Commons
R. C. Edgar,

Brie Taylor,

Victor S.-Y. Lin

et al.

Nature, Journal Year: 2022, Volume and Issue: 602(7895), P. 142 - 147

Published: Jan. 26, 2022

Public databases contain a planetary collection of nucleic acid sequences, but their systematic exploration has been inhibited by lack efficient methods for searching this corpus, which (at the time writing) exceeds 20 petabases and is growing exponentially1. Here we developed cloud computing infrastructure, Serratus, to enable ultra-high-throughput sequence alignment at petabase scale. We searched 5.7 million biologically diverse samples (10.2 petabases) hallmark gene RNA-dependent RNA polymerase identified well over 105 novel viruses, thereby expanding number known species roughly an order magnitude. characterized viruses related coronaviruses, hepatitis delta virus huge phages, respectively, analysed environmental reservoirs. To catalyse ongoing revolution viral discovery, established free comprehensive database these data tools. Expanding diversity can reveal evolutionary origins emerging pathogens improve pathogen surveillance anticipation mitigation future pandemics.

Language: Английский

Citations

386
Phage therapy: From biological mechanisms to future directions DOI Creative Commons
Steffanie A. Strathdee, Graham F. Hatfull, Vivek K. Mutalik

et al.

Cell, Journal Year: 2023, Volume and Issue: 186(1), P. 17 - 31

Published: Jan. 1, 2023

Increasing antimicrobial resistance rates have revitalized bacteriophage (phage) research, the natural predators of bacteria discovered over 100 years ago. In order to use phages therapeutically, they should (1) preferably be lytic, (2) kill bacterial host efficiently, and (3) fully characterized exclude side effects. Developing therapeutic takes a coordinated effort multiple stakeholders. Herein, we review state art in phage therapy, covering biological mechanisms, clinical applications, remaining challenges, future directions involving naturally occurring genetically modified or synthetic phages.

Language: Английский

Citations

377