Exploration of the genetic landscape of bacterial dsDNA viruses reveals an ANI gap amid extensive mosaicism DOI Creative Commons
Wanangwa Ndovie,

Jan Havránek,

Jade Leconte

et al.

mSystems, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 29, 2025

ABSTRACT Average nucleotide identity (ANI) is a widely used metric to estimate genetic relatedness, especially in microbial species delineation. While ANI calculation has been well optimized for bacteria and closely related viral genomes, accurate estimation of below 80%, particularly large reference data sets, challenging due lack scalable methods. To bridge this gap, we introduce MANIAC, an efficient computational pipeline estimating alignment fraction (AF) genomes with divergence around 70%. Using rigorous simulation framework, demonstrate MANIAC’s accuracy scalability compared existing approaches, even sets hundreds thousands genomes. Applying MANIAC curated set complete bacterial dsDNA viruses revealed multimodal distribution, distinct gap akin the (~90%) but shifted, likely viral-specific evolutionary processes such as recombination dynamics mosaicism. We then evaluated AF predictors genus-level taxonomy using logistic regression model. found that model strong predictive power (PR-AUC = 0.981), it works much better virulent 0.997) than temperate 0.847) viruses. This highlights complexity taxonomic classification phages, known their extensive mosaicism, cautions against over-reliance on cases. can be accessed at https://github.com/bioinf-mcb/MANIAC . IMPORTANCE novel called designed accurately assess average between diverse over 100k computer simulations real analyses, show could relatedness pairs 60%–70% ANI. applied investigate question discontinuity viruses, finding evidence one seen 80%. assessed ability predict genus boundaries, its virulent, not phages. Our results suggest may exhibit threshold (on 80%) above which helps maintain population cohesiveness, previously argued bacteria.

Language: Английский

The coral microbiome in sickness, in health and in a changing world DOI
Christian R. Voolstra, Jean‐Baptiste Raina, Melanie Dörr

et al.

Nature Reviews Microbiology, Journal Year: 2024, Volume and Issue: 22(8), P. 460 - 475

Published: March 4, 2024

Language: Английский

Citations

45
Megataxonomy and global ecology of the virosphere DOI Creative Commons
Eugene V. Koonin, Jens H. Kuhn, Valerian V. Dolja

et al.

The ISME Journal, Journal Year: 2024, Volume and Issue: 18(1)

Published: Jan. 1, 2024

Nearly all organisms are hosts to multiple viruses that collectively appear be the most abundant biological entities in biosphere. With recent advances metagenomics and metatranscriptomics, known diversity of substantially expanded. Comparative analysis these using advanced computational methods culminated reconstruction evolution major groups enabled construction a virus megataxonomy, which has been formally adopted by International Committee on Taxonomy Viruses. This comprehensive taxonomy consists six realms, aspired monophyletic assembled based conservation hallmark proteins involved capsid structure formation or genome replication. The different taxa differ host range accordingly ecological niches. In this review article, we outline latest developments megataxonomy discoveries will likely lead reassessment some taxa, particular, split three current realms into two more independent realms. We then discuss correspondence between distribution among niches, as well abundance versus cells habitats. across environments appears primarily determined ranges, i.e. virome is shaped composition biome given habitat, itself affected abiotic factors.

Language: Английский

Citations

25
The evolutionary drivers and correlates of viral host jumps DOI Creative Commons
Cedric C.S. Tan, Lucy van Dorp, François Balloux

et al.

Nature Ecology & Evolution, Journal Year: 2024, Volume and Issue: 8(5), P. 960 - 971

Published: March 25, 2024

Most emerging and re-emerging infectious diseases stem from viruses that naturally circulate in non-human vertebrates. When these cross over into humans, they can cause disease outbreaks, epidemics pandemics. While zoonotic host jumps have been extensively studied an ecological perspective, little attention has gone characterizing the evolutionary drivers correlates underlying events. To address this gap, we harnessed entirety of publicly available viral genomic data, employing a comprehensive suite network phylogenetic analyses to investigate mechanisms underpinning recent jumps. Surprisingly, find humans are as much source sink for spillover events, insofar infer more other animals than humans. Moreover, demonstrate heightened evolution lineages involve putative We further observe extent adaptation associated with jump is lower broader ranges. Finally, show targets natural selection vary across different families, either structural or auxiliary genes being prime selection. Collectively, our results illuminate some may contribute mitigating threats species boundaries.

Language: Английский

Citations

19
DiGAlign: Versatile and Interactive Visualization of Sequence Alignment for Comparative Genomics DOI Open Access
Yosuke Nishimura, Kohei Yamada, Yusuke Okazaki

et al.

Microbes and Environments, Journal Year: 2024, Volume and Issue: 39(1), P. n/a - n/a

Published: Jan. 1, 2024

With the explosion of available genomic information, comparative genomics has become a central approach to understanding microbial ecology and evolution. We developed DiGAlign (https://www.genome.jp/digalign/), web server that provides versatile functionality for with an intuitive interface. It allows user perform highly customizable visualization synteny map by simply uploading nucleotide sequences interest, ranging from specific region whole genome landscape microorganisms viruses. will serve wide range biological researchers, particularly experimental biologists, multifaceted features allow rapid characterization interest generation publication-ready figure.

Language: Английский

Citations

18
taxMyPhage: Automated Taxonomy of dsDNA Phage Genomes at the Genus and Species Level DOI Open Access
Andrew Millard, Rémi Denise,

Maria Lestido

et al.

PHAGE, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 24, 2025

Background: Bacteriophages are classified into genera and species based on genomic similarity, a process regulated by the International Committee Taxonomy of Viruses. With rapid increase in phage data there is growing need for automated classification systems that can handle large-scale genome analyses place phages new or existing species.

Language: Английский

Citations

2
VirClust—A Tool for Hierarchical Clustering, Core Protein Detection and Annotation of (Prokaryotic) Viruses DOI Creative Commons
Cristina Moraru

Viruses, Journal Year: 2023, Volume and Issue: 15(4), P. 1007 - 1007

Published: April 19, 2023

Recent years have seen major changes in the classification criteria and taxonomy of viruses. The current scheme, also called "megataxonomy viruses", recognizes six different viral realms, defined based on presence hallmark genes (VHGs). Within viruses are classified into hierarchical taxons, ideally by phylogeny their shared genes. To enable detection genes, first to be clustered, there is currently a need for tools assist with virus clustering classification. Here, VirClust presented. It novel, reference-free tool capable performing: (i) protein clustering, BLASTp Hidden Markov Models (HMMs) similarities; (ii) intergenomic distances calculated from content; (iii) identification core proteins (iv) annotation proteins. has flexible parameters both splitting genome tree smaller clusters, corresponding taxonomic levels. Benchmarking phage dataset showed that trees produced match ICTV at family, sub-family genus freely available, as web-service stand-alone tool.

Language: Английский

Citations

40
Virus taxonomy and the role of the International Committee on Taxonomy of Viruses (ICTV) DOI
Stuart G. Siddell, Donald B. Smith, Evelien M. Adriaenssens

et al.

Journal of General Virology, Journal Year: 2023, Volume and Issue: 104(5)

Published: May 4, 2023

The taxonomy of viruses is developed and overseen by the International Committee on Taxonomy Viruses (ICTV), which scrutinizes, approves ratifies taxonomic proposals, maintains a list virus taxa with approved names (https://ictv.global). ICTV has approximately 180 members who vote simple majority. Taxon-specific Study Groups established have combined membership over 600 scientists from wider virology community; they provide comprehensive expertise across range known are major contributors to creation evaluation proposals. Proposals can be submitted anyone will considered irrespective Group support. Thus, within community realized democratic decision-making process. upholds distinction between or replicating genetic element as physical entity taxon category it assigned. This reflected nomenclature species taxon, now mandated in binomial format (genus + epithet) typographically distinct viruses. Classification below rank (such as, genotypes strains) not remit ICTV. article, authored Executive Committee, explains principles organization, function, processes resources ICTV, aim encouraging greater understanding interaction among community.

Language: Английский

Citations

33
Taxonomic update for giant viruses in the order Imitervirales (phylum Nucleocytoviricota) DOI Open Access
Frank O. Aylward, Jônatas Santos Abrahão, Corina P. D. Brussaard

et al.

Archives of Virology, Journal Year: 2023, Volume and Issue: 168(11)

Published: Oct. 31, 2023

Language: Английский

Citations

25
Bacteriophages: A Challenge for Antimicrobial Therapy DOI Creative Commons
Nallelyt Segundo-Arizmendi,

Dafne Arellano-Maciel,

Abraham Rivera-Ramírez

et al.

Microorganisms, Journal Year: 2025, Volume and Issue: 13(1), P. 100 - 100

Published: Jan. 7, 2025

Phage therapy, which involves the use of bacteriophages (phages) to combat bacterial infections, is emerging as a promising approach address escalating threat posed by multidrug-resistant (MDR) bacteria. This brief review examines historical background and recent advancements in phage research, focusing on their genomics, interactions with host bacteria, progress medical biotechnological applications. Additionally, we expose key aspects mechanisms action, therapeutic uses considerations treating MDR infections are discussed, particularly context related virus-bacteria interactions.

Language: Английский

Citations

1
Genomic and structural insights into Jyvaskylavirus, the first giant virus isolated from Finland DOI Open Access
Gabriel Magno de Freitas Almeida, Iker Arriaga, Bruna Luiza de Azevedo

et al.

Published: Feb. 17, 2025

Giant viruses of protists are a diverse and likely ubiquitous group organisms. Here, we describe Jyvaskylavirus, the first giant virus isolated from Finland. This clade B marseillevirus was found in Acanthamoeba castellanii composting soil sample Jyväskylä, Central Its genome shares similarities with other marseilleviruses, including conserved Nucleocytoviricota genes, histone-like three unique ORFans. Helium ion microscopy electron infected cells unraveled stages Jyvaskylavirus lifecycle, such as single virions attached to cell membrane, triggering endocytosis, virus-rich vesicle formation within cytoplasm. We also reconstructed particle 6.3 Å resolution using cryo-EM. The ∼2,500 diameter virion displays structural Marseilleviridae viruses. capsid comprises 9,240 copies major protein ORF184, which possesses double jellyroll fold arranged trimers forming pseudo-hexameric capsomers. Below shell, internal membrane encloses genome. Through cross-structural -sequence comparisons AI-based software model building prediction, elucidated ORF142 penton protein, plugs twelve vertices capsid. Five additional ORFs were identified, models predicted fitted into densities that either cap capsomers externally or stabilize them internally.The isolation along virus-like particles, not only suggests these may be widespread boreal environment but provide insights extendable addressing previously lacking data on minor proteins.

Language: Английский

Citations

1