ArticleCommunications biology2021
Metagenome-assembled genomes and gene catalog from the chicken gut microbiome aid in deciphering antibiotic resistomes.
Article in Communications biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 66 papers.
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Who cites it
66 citing papers in PubMed.
- Article
- Deep-sea Microbial Dataset of the Antarctic Ocean (dsMDAO): A high-resolution deep-sea microbial dataset of the Antarctic Ocean reveals potential for taxonomic and functional diversity.Microbial genomics · 2026Article
- From environmental perception to reproductive allocation: the microbiome-membrane-mitochondria axis in poultry.Poultry science · 2026Review
- Divergent microbial functional pathways and declining redundancy in lake sediments across eutrophication gradients.Nature communications · 2026Article
- Comprehensive profiling of antibiotic resistance genes and functional clusters of orthologous groups annotation of gut microbiota in Indonesian Kedu chickens.Journal, genetic engineering & biotechnology · 2026Article
- Animal gut microbes and microbiomes in the 21st century and beyond.Science China. Life sciences · 2026Review
- Insights into antibiotic resistomes from gut meta-genome-assembled genomes of the free-range chickens.Veterinary and animal science · 2026Article
- Wastewater Metagenomic Reanalysis of Antibiotic Resistance Genes in Public Datasets from Türkiye (Ankara and Hatay).Antibiotics (Basel, Switzerland) · 2026Article
- Pooled Shotgun Metagenomics Reveals Cloacal Microbiota Composition and Resistome Patterns in Chickens from Kazakhstan.Microorganisms · 2026Article
- Prebiotics and probiotics in animal nutrition: implications for food safety, sustainability, and circular production systems.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2026Review
- Impact of soybean meal enzymatic treatment on chicken caecal microbiota and intestinal epithelial cells.Applied microbiology and biotechnology · 2026Article
- Reducing Antibiotic Dependence in Poultry: The Potential of Phytochemicals as Antibiotic Alternatives Against Bacterial Foodborne Pathogens.Tropical medicine and infectious disease · 2026Review
- A Genomic Catalog of Migratory Microbiomes from Wild Birds across China's Habitats.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- The chicken gut virome: spatial structuring and extensive diversity of 19,778 viral populations.mSystems · 2026Article
- MiGPC: a comprehensive catalog of enzybiotics from environmental metagenomes.Scientific reports · 2026Article
- Compost fermented with thermophilic Bacillaceae reduces heat stress-induced mortality in laying hens through gut microbial modulation.Animal microbiome · 2026Article
- Gut microbiota and resistome profiles of Swiss expatriates in Africa revealed by Nanopore metagenomics.Scientific reports · 2026Article
- Functional gut microbiota dynamics of generalist and specialist bacteria in association with chicken growth.ISME communications · 2026Article
- Multidimensional regulatory mechanisms of chicken immunity: focus on viral infection, intestinal microbiota and heat stress.Frontiers in veterinary science · 2026Review
- The gut resistome in poultry production: microbial ecology, antibiotic use, and sustainable control approaches.Frontiers in microbiology · 2026Review
6 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Gut microbial reference genomes and gene catalogs are necessary for understanding the chicken gut microbiome. Here, we assembled 12,339 microbial genomes and constructed a gene catalog consisting of ~16.6 million genes by integrating 799 public chicken gut microbiome samples from ten countries. We found that 893 and 38 metagenome-assembled genomes (MAGs) in our dataset were putative novel species and genera, respectively. In the chicken gut, Lactobacillus aviarius and Lactobacillus crispatus were the most common lactic acid bacteria, and glycoside hydrolases were the most abundant carbohydrate-active enzymes (CAZymes). Antibiotic resistome profiling results indicated that Chinese chicken samples harbored a higher relative abundance but less diversity of antimicrobial resistance genes (ARGs) than European samples. We also proposed the effects of geography and host species on the gut resistome. Our study provides the largest integrated metagenomic dataset from the chicken gut to date and demonstrates its value in exploring chicken gut microbial genes.
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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.