ArticleNature microbiology2019
Evaluation of a concatenated protein phylogeny for classification of tailed double-stranded DNA viruses belonging to the order Caudovirales.
Article in Nature microbiology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
66 citing papers in PubMed, 119 citations in OpenAlex.
- PhaBOX2: an enhanced web server for discovering and analyzing viral contigs in metagenomic data.Nucleic acids research · 2026Article
- Comprehensive analyses of archaeal viral genomes reveal genomic characteristics, divergence, and host interactions.Microbiome · 2026Article
- DNA viruses are constrained to ecological niches and share similar environmental adaptations with hosts.Nature communications · 2026Article
- Unveiling the biodiversity of large DNA viruses in intertidal mudflats via metagenomics.Nature communications · 2026Article
- The hidden role of rhizospheric viruses in promoting nitrogen fixation in soils.Nature communications · 2026Article
- Large-scale genomic analysis of jumbo phages: coevolution, genome architecture, and host interaction mechanisms.Animal microbiome · 2026Article
- vClassifier: a toolkit for high-resolution phylogenetic classification of prokaryotic viruses.Bioinformatics advances · 2026Article
- Characterization and genomic insights into bacteriophages Kpph1 and Kpph9 against hypervirulent carbapenem-resistantVirulence · 2025Article
- Jumbo phage-mediated transduction of genomic islands.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Virome characteristics of small mammals and their associated environments in pastoral areas on the Qinghai-Tibet Plateau.NPJ biofilms and microbiomes · 2025Article
- Role of Lysogenic Phages in the Dissemination of Antibiotic Resistance Genes Applied in the Food Chain.Foods (Basel, Switzerland) · 2025Review
- taxMyPhage: Automated Taxonomy of dsDNA Phage Genomes at the Genus and Species Level.PHAGE (New Rochelle, N.Y.) · 2025Article
- Towards a unifying phylogenomic framework for tailed phages.PLoS genetics · 2025Article
- Diversity and evolution of prokaryotic viral lytic proteins.The ISME journal · 2025Article
- Comprehensive analysis of phage genomes from diverse environments reveals their diversity, potential applications, and interactions with hosts and other phages.Frontiers in microbiology · 2025Article
- Characterization, diversity, and biogeochemical potential of soil viruses inhabiting in Yuncheng Salt Lake.Frontiers in microbiology · 2025Article
- Comprehensive genome analysis uncovers the diversity of jumbo phages in the pig gut microbiome.Frontiers in veterinary science · 2025Article
- Bacterial and viral assemblages in ulcerative colitis patients following fecal microbiota and fecal filtrate transfer.ISME communications · 2025Article
- The Last Universal Common Ancestor of Ribosome-Encoding Organisms: Portrait of LUCA.Journal of molecular evolution · 2024Review
- Unveiling the unknown viral world in groundwater.Nature communications · 2024Article
6 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Viruses of bacteria and archaea are important players in global carbon cycling as well as drivers of host evolution, yet the taxonomic classification of viruses remains a challenge due to their genetic diversity and absence of universally conserved genes. Traditional classification approaches employ a combination of phenotypic and genetic information which is no longer scalable in the era of bulk viral genome recovery through metagenomics. Here, we evaluate a phylogenetic approach for the classification of tailed double-stranded DNA viruses from the order Caudovirales by inferring a phylogeny from the concatenation of 77 single-copy protein markers using a maximum-likelihood method. Our approach is largely consistent with the International Committee on Taxonomy of Viruses, with 72 and 89% congruence at the subfamily and genus levels, respectively. Discrepancies could be attributed to misclassifications and a small number of highly mosaic genera confounding the phylogenetic signal. We also show that confidently resolved nodes in the concatenated protein tree are highly reproducible across different software and models, and conclude that the approach can serve as a framework for a rank-normalized taxonomy of most tailed double-stranded DNA viruses.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.