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Shallow metagenomics with Nanopore sequencing in canine fecal microbiota improved bacterial taxonomy and identified an uncultured CrAssphage

https://doi.org/10.1101/585067
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1016/j.chom.2018.10.002openalex-snapshot
Biology and Taxonomy of crAss-like Bacteriophages, the Most Abundant Virus in the Human Gut
inferredcites →https://doi.org/10.1016/j.tig.2014.07.001openalex-snapshot
Ten years of next-generation sequencing technology
inferredcites →https://doi.org/10.1016/j.watres.2018.08.049openalex-snapshot
Novel crAssphage marker genes ascertain sewage pollution in a recreational lake receiving urban stormwater runoff
inferredcites →https://doi.org/10.1021/acs.est.7b02703openalex-snapshot
Quantitative CrAssphage PCR Assays for Human Fecal Pollution Measurement
inferredcites →https://doi.org/10.1021/ez500266sopenalex-snapshot
Metagenomic Evaluation of the Highly Abundant Human Gut Bacteriophage CrAssphage for Source Tracking of Human Fecal Pollution
inferredcites →https://doi.org/10.1038/ismej.2010.162openalex-snapshot
Phylogenetic and gene-centric metagenomics of the canine intestinal microbiome reveals similarities with humans and mice
inferredcites →https://doi.org/10.1038/nbt.3935openalex-snapshot
Shotgun metagenomics, from sampling to analysis
inferredcites →https://doi.org/10.1038/ncomms5498openalex-snapshot
A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes
inferredcites →https://doi.org/10.1038/nmeth.3444openalex-snapshot
A complete bacterial genome assembled de novo using only nanopore sequencing data
inferredcites →https://doi.org/10.1038/nmeth.3869openalex-snapshot
DADA2: High-resolution sample inference from Illumina amplicon data
inferredcites →https://doi.org/10.1038/nmeth.f.303openalex-snapshot
QIIME allows analysis of high-throughput community sequencing data
inferredcites →https://doi.org/10.1038/nrg.2016.49openalex-snapshot
Coming of age: ten years of next-generation sequencing technologies
inferredcites →https://doi.org/10.1038/s41467-018-07225-7openalex-snapshot
ΦCrAss001 represents the most abundant bacteriophage family in the human gut and infects Bacteroides intestinalis
inferredcites →https://doi.org/10.1038/s41467-019-14103-3openalex-snapshot
Acquisition, transmission and strain diversity of human gut-colonizing crAss-like phages
inferredcites →https://doi.org/10.1038/s41564-017-0053-yopenalex-snapshot
Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut
inferredcites →https://doi.org/10.1038/s41587-018-0004-zopenalex-snapshot
Errors in long-read assemblies can critically affect protein prediction
inferredcites →https://doi.org/10.1038/s41587-019-0202-3openalex-snapshot
Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery
inferredcites →https://doi.org/10.1038/s41587-020-0422-6openalex-snapshot
Complete, closed bacterial genomes from microbiomes using nanopore sequencing
inferredcites →https://doi.org/10.1093/bioinformatics/btr087openalex-snapshot
PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers
inferredcites →https://doi.org/10.1093/bioinformatics/bty191openalex-snapshot
Minimap2: pairwise alignment for nucleotide sequences
inferredcites →https://doi.org/10.1093/gigascience/giz043openalex-snapshot
Ultra-deep, long-read nanopore sequencing of mock microbial community standards
inferredcites →https://doi.org/10.1093/nar/gkw387openalex-snapshot
PHASTER: a better, faster version of the PHAST phage search tool
inferredcites →https://doi.org/10.1101/030742openalex-snapshot
What’s in my pot? Real-time species identification on the MinION™
inferredcites →https://doi.org/10.1101/180406openalex-snapshot
Rapid profiling of the preterm infant gut microbiota using nanopore sequencing aids pathogen diagnostics
inferredcites →https://doi.org/10.1101/299537openalex-snapshot
ampvis2: an R package to analyse and visualise 16S rRNA amplicon data
inferredcites →https://doi.org/10.1101/456905openalex-snapshot
Nanopore sequencing enables high-resolution analysis of resistance determinants and mobile elements in the human gut microbiome
inferredcites →https://doi.org/10.1101/465328openalex-snapshot
Improving recovery of member genomes from enrichment reactor microbial communities using MinION–based long read metagenomics
inferredcites →https://doi.org/10.1101/527796openalex-snapshot
Global phylogeography and ancient evolution of the widespread human gut virus crAssphage
inferredcites →https://doi.org/10.1101/gr.210641.116openalex-snapshot
Centrifuge: rapid and sensitive classification of metagenomic sequences
inferredcites →https://doi.org/10.1101/gr.215087.116openalex-snapshot
Canu: scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separation
inferredcites →https://doi.org/10.1111/1751-7915.12841openalex-snapshot
Determination of crAssphage in water samples and applicability for tracking human faecal pollution
inferredcites →https://doi.org/10.1128/aem.03006-05openalex-snapshot
Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
inferredcites →https://doi.org/10.1186/s40168-018-0450-3openalex-snapshot
Similarity of the dog and human gut microbiomes in gene content and response to diet
inferredcites →https://doi.org/10.12688/f1000research.16817.1openalex-snapshot
Microbiota profiling with long amplicons using Nanopore sequencing: full-length 16S rRNA gene and whole rrn operon
inferredcites →https://doi.org/10.1371/journal.pone.0057923openalex-snapshot
The Variability of the 16S rRNA Gene in Bacterial Genomes and Its Consequences for Bacterial Community Analyses
inferredcites →https://doi.org/10.1371/journal.pone.0226930openalex-snapshot
Biogeographic study of human gut-associated crAssphage suggests impacts from industrialization and recent expansion
inferredcites →https://doi.org/10.2807/1560-7917.es.2018.23.50.1800228openalex-snapshot
Assessment of metagenomic Nanopore and Illumina sequencing for recovering whole genome sequences of chikungunya and dengue viruses directly from clinical samples
inferredcites →https://doi.org/10.7488/ds/2470openalex-snapshot
The genomic and proteomic landscape of the rumen microbiome revealed by comprehensive genome-resolved metagenomics
inferredcites →https://doi.org/10.7717/peerj.6800openalex-snapshot
Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1002/edn3.70009openalex-snapshot
Evaluation of a Nanopore Sequencing Strategy on Bacterial Communities From Marine Sediments
inferred← citeshttps://doi.org/10.1101/2019.12.20.884395openalex-snapshot
Applying Nanopore sequencing to a One-Health scenario for colistin resistance transmission among pigs, cows and the farmer
inferred← citeshttps://doi.org/10.1101/2020.10.08.329714openalex-snapshot
Hybrid assembly of an agricultural slurry virome reveals a diverse and stable community with the potential to alter the metabolism and virulence of veterinary pathogens
inferred← citeshttps://doi.org/10.1101/2023.06.06.541006openalex-snapshot
Fine-scale congruence in bacterial community structure from marine sediments sequenced by short-reads on Illumina and long-reads on Nanopore
inferred← citeshttps://doi.org/10.1186/s12864-021-07607-0openalex-snapshot
Long-read metagenomics retrieves complete single-contig bacterial genomes from canine feces
inferred← citeshttps://doi.org/10.1186/s12864-021-08046-7openalex-snapshot
The mitochondrial genome and Epigenome of the Golden lion Tamarin from fecal DNA using Nanopore adaptive sequencing
inferred← citeshttps://doi.org/10.1186/s40168-021-01010-3openalex-snapshot
Hybrid assembly of an agricultural slurry virome reveals a diverse and stable community with the potential to alter the metabolism and virulence of veterinary pathogens
inferred← citeshttps://doi.org/10.17605/osf.io/2f8w7openalex-snapshot
Preprint - Applying Nanopore sequencing to a One-Health scenario for colistin resistance transmission among pigs, cows and the farmer
inferred← citeshttps://doi.org/10.3389/fcimb.2025.1701570openalex-snapshot
Nanopore sequencing in veterinary medicine: from concepts to clinical applications
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