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References from Insights into antibiotic resistomes from gut meta-genome-assembled genomes of the free-range chickens. Local targets link to admitted publications; unresolved targets remain external evidence.
Binning metagenomic contigs by coverage and composition
10.1038/nmeth.3103 · 2014 · External reference
The Gut microbiome as a reservoir for antimicrobial resistance
10.1093/infdis/jiaa497 · 2021 · External reference
Gut Metagenome Reveals the Microbiome Signatures in Tibetan and Black Pigs
10.3390/ani15050753 · 2025 · External reference
Metagenomic profiling uncovers microbiota and antibiotic resistance patterns across human, chicken, pig fecal, and soil environments
10.1016/j.scitotenv.2024.174734 · 2024 · External reference
Antibiotic resistance in Pseudomonas aeruginosa - Mechanisms, epidemiology and evolution
10.1016/j.drup.2019.07.002 · 2019 · External reference
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
10.1038/nbt.3893 · 2017 · External reference
Fast and sensitive protein alignment using DIAMOND
10.1038/nmeth.3176 · 2015 · External reference
MAGqual: a stand-alone pipeline to assess the quality of metagenome-assembled genomes
10.1186/s40168-024-01949-z · 2024 · External reference
Gut microbial diversity analysis of different native chickens and screening of chicken-derived probiotics
10.3390/ani13233672 · 2023 · External reference
fastp: an ultra-fast all-in-one FASTQ preprocessor
10.1093/bioinformatics/bty560 · 2018 · External reference
Origins and evolution of antibiotic resistance
10.1128/mmbr.00016-10 · 2010 · External reference
Microbiota, gut health and chicken productivity: what is the connection?
10.3390/microorganisms7100374 · 2019 · External reference
Forecasting the dissemination of antibiotic resistance genes across bacterial genomes
10.1038/s41467-021-22757-1 · 2021 · External reference
Metagenome-assembled genomes and gene catalog from the chicken gut microbiome aid in deciphering antibiotic resistomes
10.1038/s42003-021-02827-2 · 2021 · External reference
Quantitative microbiome profiling reveals the developmental trajectory of the chicken gut microbiota and its connection to host metabolism
10.1002/imt2.105 · 2023 · External reference
Strain-level characterization of broad host range mobile genetic elements transferring antibiotic resistance from the human microbiome
10.1038/s41467-022-29096-9 · 2022 · External reference
The microbiome protocols ebook initiative: building a bridge to microbiome research
10.1002/imt2.182 · 2024 · External reference
Insights into antibiotic resistomes from metagenome-assembled genomes and gene catalogs of soil microbiota across environments
10.7717/peerj.20348 · 2025 · External reference
IS26 and the IS26 family: versatile resistance gene movers and genome reorganizers
10.1128/mmbr.00119-22 · 2024 · External reference
Structures bounded by directly-oriented members of the IS26 family are pseudo-compound transposons
10.1016/j.plasmid.2020.102530 · 2020 · External reference
Comparison of antimicrobial resistant genes in chicken gut microbiome grown on organic and conventional diet
10.1016/j.vas.2016.07.001 · 2016 · External reference
The Presence of Stone Moroko (Pseudorasbora parva) drives divergent sediment resistome profiles in chinese mitten crab (eriocheir sinensis) polyculture pond
10.3390/foods14213626 · 2025 · External reference
Bacterial multidrug efflux pumps at the frontline of antimicrobial resistance: an overview
10.3390/antibiotics11040520 · 2022 · External reference
The chicken gut metagenome and the modulatory effects of plant-derived benzylisoquinoline alkaloids
10.1186/s40168-018-0590-5 · 2018 · External reference
Prodigal: prokaryotic gene recognition and translation initiation site identification
10.1186/1471-2105-11-119 · 2010 · External reference
The distribution of antibiotic resistance genes in chicken gut microbiota commensals
10.1038/s41598-021-82640-3 · 2021 · External reference
MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities
10.7717/peerj.1165 · 2015 · External reference
High diversity and abundance of cultivable tetracycline-resistant bacteria in soil following pig manure application
10.1038/s41598-018-20050-8 · 2018 · External reference
Genome-resolved metagenomics using environmental and clinical samples
10.1093/bib/bbab030 · 2021 · External reference
Genome-resolved metagenomics: a game changer for microbiome medicine
10.1038/s12276-024-01262-7 · 2024 · External reference
Resistome Analysis of Global Livestock and Soil Microbiomes
10.3389/fmicb.2022.897905 · 2022 · External reference
Single nucleus/cell RNA-seq of the chicken hypothalamic-pituitary-ovarian axis offers new insights into the molecular regulatory mechanisms of ovarian development
10.24272/j.issn.2095-8137.2024.037 · 2024 · External reference
MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
10.1093/bioinformatics/btv033 · 2015 · External reference
Fast and accurate short read alignment with Burrows-Wheeler transform
10.1093/bioinformatics/btp324 · 2009 · External reference
Livestock and poultry breeding farms as a fixed and underestimated source of antibiotic resistance genes
10.1007/s11356-024-34413-4 · 2024 · External reference
Host immune constraints delineate the window of microbial colonization during early development of Larimichthys crocea
2026 · External reference
Analysis of compositions of microbiomes with bias correction
10.1038/s41467-020-17041-7 · 2020 · External reference
Antibiotic resistance genes in antibiotic-free chicken farms
10.3390/antibiotics9030120 · 2020 · External reference
dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication
10.1038/ismej.2017.126 · 2017 · External reference
Mash: fast genome and metagenome distance estimation using MinHash
10.1186/s13059-016-0997-x · 2016 · External reference
The structure and diversity of human, animal and environmental resistomes
10.1186/s40168-016-0199-5 · 2016 · External reference
A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life
10.1038/nbt.4229 · 2018 · External reference
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
10.1101/gr.186072.114 · 2015 · External reference
Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life
10.1038/s41564-017-0012-7 · 2017 · External reference
Antimicrobial resistance: Prevalence, economic burden, mechanisms of resistance and strategies to overcome
10.1016/j.ejps.2021.106103 · 2022 · External reference
Prediction of the intestinal resistome by a three-dimensional structure-based method
10.1038/s41564-018-0292-6 · 2019 · External reference
Genome-resolved metagenomics of the chicken gut microbiome
10.3389/fmicb.2021.726923 · 2021 · External reference
Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy
10.1038/s41564-018-0171-1 · 2018 · External reference
Association of female reproductive tract microbiota with egg production in layer chickens
10.1093/gigascience/giab067 · 2021 · External reference
Metagenomic tools in microbial ecology research
10.1016/j.copbio.2021.01.019 · 2021 · External reference
Core and variable antimicrobial resistance genes in the gut microbiomes of Chinese and European pigs
10.24272/j.issn.2095-8137.2023.012 · 2024 · External reference
Insights into left-right asymmetric development of chicken ovary at the single-cell level
10.1016/j.jgg.2024.08.002 · 2024 · External reference
Multiomics analysis provides insights into musk secretion in muskrat and musk deer
10.1093/gigascience/giaf006 · 2025 · External reference
Dihydroartemisinin inhibits plasmid transfer in drug-resistant Escherichia coli via limiting energy supply
10.24272/j.issn.2095-8137.2023.084 · 2023 · External reference
More diversified antibiotic resistance genes in chickens and workers of the live poultry markets
10.1016/j.envint.2021.106534 · 2021 · External reference
Impact of contrasting poultry exposures on human, poultry, and wastewater antibiotic resistomes in Bangladesh
10.1128/spectrum.01763-23 · 2023 · External reference
Early life dynamics of ARG and MGE associated with intestinal virome in neonatal piglets
10.1016/j.vetmic.2022.109575 · 2022 · External reference
MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets
2016 · External reference
The abundance and diversity of antibiotic resistance genes in layer chicken ceca is associated with farm enviroment
10.3389/fmicb.2023.1177404 · 2023 · External reference
KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases
10.1093/nar/gkr483 · 2011 · External reference
Metagenomic analysis reveals the microbiome and antibiotic resistance genes in indigenous Chinese yellow-feathered chickens
2022 · External reference
Metagenomic Insights into Chicken Gut Antibiotic Resistomes and Microbiomes
10.1128/spectrum.01907-21 · 2022 · External reference
Deciphering comprehensive profiles of pathogenies and resistome of pork using integrating metagenomic and isolation strategies
10.1002/imo2.70004 · 2025 · External reference
Mobile genetic elements mediate the cross-media transmission of antibiotic resistance genes from pig farms and their risks
10.1016/j.scitotenv.2024.172115 · 2024 · External reference
Co-occurrence and co-expression of antibiotic, biocide, and metal resistance genes with mobile genetic elements in microbial communities subjected to long-term antibiotic pressure: Novel insights from metagenomics and metatranscriptomics
10.1016/j.jhazmat.2025.137559 · 2025 · External reference
Improved microbial genomes and gene catalog of the chicken gut from metagenomic sequencing of high-fidelity long reads
10.1093/gigascience/giac116 · 2022 · External reference
Geographic patterns of antibiotic resistance in the human gut microbiome: insights from metagenome-assembled genomes across four Chinese provinces
10.3389/fmicb.2025.1652757 · 2025 · External reference
Functional cloning and characterization of antibiotic resistance genes from the chicken gut microbiome
10.1128/aem.06920-11 · 2012 · External reference
Distribution of antibiotic resistance genes in the environment
10.1016/j.envpol.2021.117402 · 2021 · External reference
A comparative atlas of single-cell chromatin accessibility in the human brain
10.1126/science.adf7044 · 2023 · External reference
Vaginal microbiota are associated with in vitro fertilization during female infertility
10.1002/imt2.185 · 2024 · External reference
Inter-plasmid transfer of antibiotic resistance genes accelerates antibiotic resistance in bacterial pathogens
10.1093/ismejo/wrad032 · 2024 · External reference
The multi-kingdom microbiome catalog of the chicken gastrointestinal tract
10.1016/j.bsheal.2024.02.006 · 2024 · External reference
Dynamic Changes in the Gut Microbial Community and Function during Broiler Growth
10.1128/spectrum.01005-22 · 2022 · External reference