Table_3_Metagenomic analysis reveals the microbiome and antibiotic resistance genes in indigenous Chinese yellow-feathered chickens.xlsx

Yellow-feathered chickens have great nutritional value and are widely and traditionally used in China, on an industrial scale as broilers. The presence of intestinal microbes has been shown to correlate with poultry performance and serves as an essential reservoir of antibiotic resistance genes (ARGs). Antibiotic resistance is a major public health concern. Here, we investigated functional characteristics of the gut microbiome of indigenous Chinese yellow-feathered chickens (the Huiyang Bearded, Xinghua, Huaixiang, Zhongshan Shanlan, Qingyuan Partridge, and Yangshan chickens) through metagenomic sequencing and reconstructed 409 draft genomes, including 60 novel species and 6 novel genera. Furthermore, we assessed the functions of the intestinal microbial communities and examined the ARGs within them. The results showed that the microbial populations of yellow-feathered broilers were primarily dominated by Bacteroidetes and Firmicutes at the phylum level and Bacteroides at the genus level. Furthermore, the Qingyuan Partridge chicken showed a significantly higher abundance of Prevotella than the other five breeds of chicken. Principal coordinates analysis indicated significant differences in the structures of microbial communities and ARGs, based on the binary Jaccard distance, among the six chicken breeds. Moreover, 989 ARGs conferring tetracycline, multidrug, and aminoglycoside resistance were identified, which represented more than 80% of the faecal resistomes; the most abundant gene in the yellow-feathered chickens was tet(Q). In addition, we found the greatest abundance of resistance genes in Xinghua chickens, indicating that Xinghua chickens are highly resistant to antibiotics. Overall, our findings revealed differences in the gut microbial community structure of indigenous Chinese yellow-feathered broiler breeds and the composition and characteristics of ARGs and antibiotic resistance that enabled us to reconstruct the yellow-feathered chicken gut microbial community genomes. The current data significantly improves our knowledge of the gut microbiome and antibiotic resistance of popular broiler breeds in China.

黄羽鸡营养价值出众，在中国拥有悠久广泛的传统应用场景，且已作为肉鸡实现规模化工业养殖。肠道微生物组已被证实与家禽生产性能紧密相关，同时是抗生素抗性基因 (antibiotic resistance genes, ARGs) 的重要储存库。抗生素耐药性已成为重大公共卫生安全隐患。本研究通过宏基因组测序，对6种中国地方黄羽鸡（惠阳胡须鸡、杏花鸡、怀乡鸡、中山沙栏鸡、清远麻鸡及阳山鸡）的肠道微生物组功能特性展开探究，共重建得到409个草图基因组 (draft genome)，其中包含60个新物种与6个新属。此外，本研究还对肠道微生物群落的功能进行了评估，并对其中的抗生素抗性基因展开了检测。研究结果显示，在门分类水平上，黄羽肉鸡的肠道微生物种群主要以拟杆菌门 (Bacteroidetes) 和厚壁菌门 (Firmicutes) 为主；在属分类水平上则以拟杆菌属 (Bacteroides) 为优势菌属。此外，清远麻鸡的普雷沃菌属 (Prevotella) 丰度显著高于其余5个鸡种。基于二元雅卡尔距离 (binary Jaccard distance) 的主坐标分析 (Principal coordinates analysis, PCoA) 结果显示，6个鸡种的肠道微生物群落结构与抗生素抗性基因组成均存在显著差异。此外，本研究共鉴定出989种可赋予四环素、多药及氨基糖苷类抗生素抗性的抗生素抗性基因，其占粪便耐药组 (faecal resistomes) 的比例超过80%；黄羽鸡中丰度最高的抗性基因为tet(Q)。此外，研究发现杏花鸡的抗性基因丰度最高，表明其对抗生素具有较高的耐药性。综上，本研究揭示了中国地方黄羽肉鸡品种的肠道微生物群落结构差异，以及抗生素抗性基因的组成与特征，并成功重建了黄羽鸡肠道微生物群落基因组。本研究数据显著深化了我们对中国主流肉鸡品种肠道微生物组与抗生素耐药性的认知。