State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China.
College of Veterinary Medicine, Henan Agricultural University, 450046, Zhengzhou, Henan, China.
Commun Biol. 2021 Nov 18;4(1):1305. doi: 10.1038/s42003-021-02827-2.
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.
肠道微生物参考基因组和基因目录对于了解鸡肠道微生物组是必要的。在这里，我们整合了来自十个国家的 799 个公共鸡肠道微生物组样本，组装了 12339 个微生物基因组，并构建了一个包含约 1660 万个基因的基因目录。我们发现，在我们的数据集，893 个和 38 个宏基因组组装基因组（MAGs）分别是可能的新物种和属。在鸡肠道中，嗜酸乳杆菌和短乳杆菌是最常见的乳酸菌，糖苷水解酶是最丰富的碳水化合物活性酶（CAZymes）。抗生素抗性组分析结果表明，与欧洲样本相比，中国鸡样本含有更高相对丰度但更少多样性的抗菌药物抗性基因（ARGs）。我们还提出了地理和宿主种类对肠道抗性组的影响。我们的研究提供了迄今为止最大的鸡肠道综合宏基因组数据集，并展示了其在探索鸡肠道微生物基因方面的价值。
