The untapped potential of phage model systems as therapeutic agents DOI Creative Commons
Jordan Romeyer Dherbey, Frederic Bertels

Virus Evolution, Год журнала: 2024, Номер 10(1)

Опубликована: Янв. 1, 2024

Abstract With the emergence of widespread antibiotic resistance, phages are an appealing alternative to antibiotics in fight against multidrug-resistant bacteria. Over past few years, many have been isolated from various environments treat bacterial pathogens. While isolating novel for treatment has had some success compassionate use, developing into a general therapeutic will require considerable time and financial resource investments. These investments may be less significant well-established phage model systems. The knowledge acquired decades research on their structure, life cycle, evolution ensures safe application efficient handling. However, one major downside established systems is inability infect pathogenic This problem not insurmountable; host range can extended through genetic engineering or experiments. In future, breeding pathogens could provide new avenue develop agents.

Язык: Английский

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

и другие.

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

Процитировано

1044
VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses DOI Creative Commons
Jiarong Guo, Benjamin Bolduc, Ahmed A. Zayed

и другие.

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

Процитировано

815
Global Organization and Proposed Megataxonomy of the Virus World DOI Open Access
Eugene V. Koonin, Valerian V. Dolja, Mart Krupovìč

и другие.

Microbiology and Molecular Biology Reviews, Год журнала: 2020, Номер 84(2)

Опубликована: Март 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.

Язык: Английский

Процитировано

532
The human virome: assembly, composition and host interactions DOI Open Access
Guanxiang Liang, Frederic D. Bushman

Nature Reviews Microbiology, Год журнала: 2021, Номер 19(8), С. 514 - 527

Опубликована: Март 30, 2021

Язык: Английский

Процитировано

429
A catalog of tens of thousands of viruses from human metagenomes reveals hidden associations with chronic diseases DOI Creative Commons
Michael J. Tisza, Christopher B. Buck

Proceedings of the National Academy of Sciences, Год журнала: 2021, Номер 118(23)

Опубликована: Июнь 3, 2021

Significance Mechanisms of many human chronic diseases involve abnormal action the immune system and/or altered metabolism. The microbiome, an important regulator metabolic and immune-related phenotypes, has been shown to be associated with or participate in development a variety diseases. Viruses bacteria (i.e., “phages”) are ubiquitous mysterious, several studies have that phages exert great control over behavior—and misbehavior—of their host bacteria. This study uses techniques discover analyze 45,000 viruses bodies. abundance 2,000 specific is found correlate common

Язык: Английский

Процитировано

193
BACPHLIP: predicting bacteriophage lifestyle from conserved protein domains DOI Creative Commons
Adam J. Hockenberry, Claus O. Wilke

PeerJ, Год журнала: 2021, Номер 9, С. e11396 - e11396

Опубликована: Май 6, 2021

Bacteriophages are broadly classified into two distinct lifestyles: temperate and virulent. Temperate phages capable of a latent phase infection within host cell (lysogenic cycle), whereas virulent directly replicate lyse cells upon (lytic cycle). Accurate lifestyle identification is critical for determining the role individual phage species ecosystems their effect on evolution. Here, we present BACPHLIP, BACterioPHage LIfestyle Predictor. BACPHLIP detects presence set conserved protein domains an input genome uses this data to predict via Random Forest classifier that was trained dataset 634 genomes. On independent test 423 phages, has accuracy 98% greatly exceeding previously existing tools (79%). freely available GitHub ( https://github.com/adamhockenberry/bacphlip ) code used build provided in separate repository https://github.com/adamhockenberry/bacphlip-model-dev users wishing interrogate re-train underlying classification model.

Язык: Английский

Процитировано

192
Cressdnaviricota : a Virus Phylum Unifying Seven Families of Rep-Encoding Viruses with Single-Stranded, Circular DNA Genomes DOI
Mart Krupovìč, Arvind Varsani, Darius Kazlauskas

и другие.

Journal of Virology, Год журнала: 2020, Номер 94(12)

Опубликована: Апрель 7, 2020

ou non, émanant des établissements d'enseignement et de recherche français étrangers, laboratoires publics privés.

Процитировано

152
Cenote-Taker 2 democratizes virus discovery and sequence annotation DOI Creative Commons
Michael J. Tisza, Anna K. Belford, Guillermo Domínguez-Huerta

и другие.

Virus Evolution, Год журнала: 2020, Номер 7(1)

Опубликована: Дек. 8, 2020

Abstract Viruses, despite their great abundance and significance in biological systems, remain largely mysterious. Indeed, the vast majority of perhaps hundreds millions viral species on planet undiscovered. Additionally, many viruses deposited central databases like GenBank RefSeq are littered with genes annotated as ‘hypothetical protein’ or equivalent. Cenote-Taker 2, a virus discovery annotation tool available command line graphical user interface free high-performance computation access, utilizes highly sensitive models hallmark to discover familiar divergent sequences from user-input contigs. 2 uses flexible set modules automatically annotate sequence features contigs, providing more gene information than comparable tools. The outputs include readable interactive genome maps, virome summary tables, files that can be directly submitted GenBank. We expect facilitate discovery, annotation, expansion known virome.

Язык: Английский

Процитировано

118
The LUCA and its complex virome DOI
Mart Krupovìč, Valerian V. Dolja, Eugene V. Koonin

и другие.

Nature Reviews Microbiology, Год журнала: 2020, Номер 18(11), С. 661 - 670

Опубликована: Июль 14, 2020

Язык: Английский

Процитировано

101
Global genome analysis reveals a vast and dynamic anellovirus landscape within the human virome DOI Creative Commons
Cesar Arze, Simeon Springer, Gytis Dudas

и другие.

Cell Host & Microbe, Год журнала: 2021, Номер 29(8), С. 1305 - 1315.e6

Опубликована: Июль 27, 2021

Anelloviruses are a ubiquitous component of healthy human viromes and remain highly prevalent after being acquired early in life. The full extent "anellome" diversity its evolutionary dynamics unexplored. We employed in-depth sequencing blood-transfusion donor(s)-recipient pairs coupled with public genomic resources for large-scale assembly anellovirus genomes used the data to characterize global personal through time. breadth anellome is much greater than previously appreciated, individuals harbor unique anellomes transmit lineages that can persist several months within diverse milieu endemic host lineages. Anellovirus sequence shaped by extensive recombination at all levels divergence, hindering traditional phylogenetic analyses. Our findings illuminate transmission vast anelloviruses set foundation future studies their biology.

Язык: Английский

Процитировано

79