Metagenome-assembled genomes and gene catalog from the chicken gut microbiome aid in deciphering antibiotic resistomes

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.

The Core Human Microbiome: Does It Exist and How Can We Find It? A Critical Review of the Concept

“…These include healthy Westerners from the US (HMP phases 1, 2, and 3) [ 9 , 37 ] and Denmark (MetaHIT), individuals with IBD from Spain (MetaHIT) [ 28 ], and a group of hunter-gatherers and traditional Bantu agriculturalists from the Central Africa Republic [ 38 ]. As controls, we consider fecal samples from gorillas [ 38 ], mice [ 39 ], and chickens [ 40 ]. Community composition was evaluated using MetaPhlan3, and functional profiles were generated using HUMAnN3 [ 41 ] (see Supplementary Information for more details).…”

“…The following supporting information can be downloaded at: https: //www.mdpi.com/article/10.3390/nu14142872/s1, Figure S1: Functional profiling of eight cohorts; Table S1: Summary of information of the data that was used for the community and function analyses; Table S2: Statistics of samples related to the human microbiome; Table S3: fraction of samples in each cohort in which the species was identified; Table S4: UniRef90 clusters that are present at ≥90% of the samples of at least one cohort; Table S5: all MetaCyc pathways detected in at least one sample. References [9,28,[37][38][39][40][41]216] are cited in the supplementary materials.…”

Metagenomic analysis reveals the microbiome and antibiotic resistance genes in indigenous Chinese yellow-feathered chickens

“…The global consumption of antibiotics used for chickens, pigs, and cattle is estimated to increase by 67%, from 63,151 t in 2010 to 105,596 t in 2030 ( Van Boeckel et al, 2015 ). Improper use of antibiotics in various environments has led to the spread of ARGs in China ( Qiao et al, 2018 ; Glendinning et al, 2020 ; Feng et al, 2021 ). The frequent use of antibiotics in livestock animals and humans results in the propagation of ARGs and is becoming a major global health issue.…”

Progress and opportunities through use of genomics in animal production

“…The composition of these communities also has a significant effect on high value characteristics, such as feed efficiency and environmental emission (e.g., methane production in ruminants) and the health of the animal. These interactions have been explored in several farmed species, including poultry [112][113][114], pigs [115,116], cattle, sheep and deer [111,[117][118][119][120][121][122]. As further advances are made with in-vivo (e.g.…”