ArticleGenome biology2019
Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation.
Article in Genome biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 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
65 citing papers in PubMed.
- Rumen DNA virome plasticity and viral metabolic potential are associated with seasonal adaptation in grazing yak and cattle on the Qinghai-Tibet Plateau.Journal of animal science and biotechnology · 2026Article
- Evidence tiers for strain-resolved long-read metagenomics.iMetaOmics · 2026Article
- Article
- Hi-C Metagenome Deconvolution of Double-Crested Cormorant (Microorganisms · 2026Article
- Unraveling plasmid contributions to phosphorus acquisition in soil microbiomes.Environmental microbiome · 2026Article
- Hi-C Links Reveal Viral Activity and Infection Within the Free-Living Microbial Community of a Secondary Chlorophyll Maximum in the Eastern Tropical North Pacific.Environmental microbiology · 2026Article
- Benchmarking alignment strategies for Hi-C reads in metagenomic Hi-C data.Genome biology · 2026Article
- Diversity and ecological roles of hidden viral players in groundwater microbiomes.Nature communications · 2026Article
- Review
- Quantifying human-environment interactions through Bayesian modeling of species-resolved microbial transfer signatures: an exploratory proof-of-concept study.Frontiers in microbiology · 2026Article
- Benchmarking with synthetic communities provides a baseline for virus-host inferences from Hi-C proximity linking.PLoS biology · 2025Article
- Phages with a broad host range are common across ecosystems.Nature microbiology · 2025Article
- Synthetic community Hi-C benchmarking provides a baseline for virus-host inferences.bioRxiv : the preprint server for biology · 2025Article
- The prototypic crAssphage is a linear phage-plasmid.Cell host & microbe · 2025Article
- Leveraging the microbiome to combat antibiotic resistant gynecological infections.npj antimicrobials and resistance · 2025Review
- Review
- Efficient and easy-to-use capturing three-dimensional metagenome interactions with GutHi-C.iMeta · 2024Article
- Decoupling of strain- and intrastrain-level interactions of microbiomes in a sponge holobiont.Nature communications · 2024Article
- Distributions, interactions, and dynamics of prokaryotes and phages in a hybrid biological wastewater treatment system.Microbiome · 2024Article
- Reference-free structural variant detection in microbiomes via long-read co-assembly graphs.Bioinformatics (Oxford, England) · 2024Article
5 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
21 authors.
Funding
Abstract
We describe a method that adds long-read sequencing to a mix of technologies used to assemble a highly complex cattle rumen microbial community, and provide a comparison to short read-based methods. Long-read alignments and Hi-C linkage between contigs support the identification of 188 novel virus-host associations and the determination of phage life cycle states in the rumen microbial community. The long-read assembly also identifies 94 antimicrobial resistance genes, compared to only seven alleles in the short-read assembly. We demonstrate novel techniques that work synergistically to improve characterization of biological features in a highly complex rumen microbial community.
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.