肉鸽肠道微生物菌群差异分析和抗生素耐药基因预测

doi:10.11843/j.issn.0366-6964.2023.12.037

畜牧兽医学报 ›› 2023, Vol. 54 ›› Issue (12): 5293-5300.doi: 10.11843/j.issn.0366-6964.2023.12.037

肉鸽肠道微生物菌群差异分析和抗生素耐药基因预测

陶洁^1,2,3, 李本强^1,2,3, 程靖华^1,2,3, 石迎^1,2,3, 刘佩红^1,2,3, 刘惠莉^1,2,3*

1. 上海市农业科学院畜牧兽医研究所, 上海 201106;
2. 上海市农业遗传育种重点实验室, 上海 201106;
3. 农业农村部区域特色畜禽品种疾病防控重点实验室(部省共建), 上海 201106

收稿日期:2023-04-24 出版日期:2023-12-23 发布日期:2023-12-26
通讯作者: 刘惠莉,主要从事动物疾病诊断与防控研究,E-mail:huilil@163.com
作者简介:陶洁(1986-),女,江苏张家港人,博士,副研究员,主要从事动物疾病防控研究,E-mail:livia_taojie@126.com
基金资助:
上海市肉鸽产业技术体系(沪农科产字(2022)第12号);动物疾病防控团队(沪农科卓[2022]012)

Differential Analysis and the Antibiotic Resistance Genes Prediction of Gut Microbiota in Pigeon

TAO Jie^1,2,3, LI Benqiang^1,2,3, CHENG Jinghua^1,2,3, SHI Ying^1,2,3, LIU Peihong^1,2,3, LIU Huili^1,2,3*

1. Institute of Animal Husbandry and Veterinary Medicine, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China;
2. Shanghai Key Laboratory of Agricultural Genetic Breeding, Shanghai 201106, China;
3. Key Laboratory for Disease Prevention and Control of Regional Characteristics Livestock and Poultry Breeds of the Ministry of Agriculture and Rural Affairs (Jointly Established by the Ministry and Province), Shanghai 201106, China

Received:2023-04-24 Online:2023-12-23 Published:2023-12-26

摘要/Abstract

摘要： 本研究旨在利用宏基因组学深入分析上海某鸽场青年鸽(RP)和产鸽(LP)粪便样品的微生物菌群差异。结果显示,肉鸽肠道菌群的优势菌门为厚壁菌(Firmicutes)、变形菌(Proteobacteria)和放线菌(Actinobacteria)。RP组中双歧杆菌(Bifidobacterium)、棒状杆菌(Corynebacteriun)、嗜冷杆菌(Psychrobacter)、链球菌属(Streptococcus)含量显著高于LP组,而LP组金黄色葡萄球菌属(Staphyloccus)、短状杆菌属(Brachybacterium)、库特氏菌属(Kurthia)和埃希氏菌属(Escherichia)含量显著高于RP组。LEfSe分析显示,LP和RP组的差异表达基因主要富集于5个KEGG通路。抗生素耐药基因(antibiotic resistance genes,ARGs)鉴定显示,肉鸽体内存在198种ARGs,其中多重耐药类ARGs流行率40%以上,说明该场肉鸽抗生素耐药情况较严重。本研究为后续深入研究肠道菌群与健康养殖、抗生素耐药机制等提供了科学数据。

关键词: 肉鸽, 宏基因组学, 肠道菌群, 抗生素耐药基因

Abstract: In this study, metagenomics was used to explore the fecal microbiota differences between the young pigeons (RP) and older pigeons (LP). The results showed that Firmicutes, Proteobacteria and Actinobacteria were the dominant bacterias. The contents of Bifidobacterium, Corynebacteriun, Psychrobacter and Streptococcus in RP group were significantly higher than those in LP group, while the relative abundance of Staphyloccus, Brachybacterium, Kurthia and Escherichia in LP group were significantly higher than those in RP group. Further LEfSe analysis showed that the differentially expressed genes in the two groups were enriched in 5 KEGG pathways. Antibiotic resistance genes (ARGs) analyzation showed that a total of 198 ARG,were identified. And the prevalence rate of multi-drug ARGs was more than 40%, which indicated that the antibiotic resistance problem in pigeon is seriously. The current study provided scientific datas for further researches on gut microflora and healthy breeding, and mechanism of antibiotic resistance mechanism.

Key words: pigeon, metagenomics, gut microbiota, antibiotic resistance gene

中图分类号:

S836

陶洁, 李本强, 程靖华, 石迎, 刘佩红, 刘惠莉. 肉鸽肠道微生物菌群差异分析和抗生素耐药基因预测[J]. 畜牧兽医学报, 2023, 54(12): 5293-5300.

TAO Jie, LI Benqiang, CHENG Jinghua, SHI Ying, LIU Peihong, LIU Huili. Differential Analysis and the Antibiotic Resistance Genes Prediction of Gut Microbiota in Pigeon[J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(12): 5293-5300.

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肉鸽肠道微生物菌群差异分析和抗生素耐药基因预测

Differential Analysis and the Antibiotic Resistance Genes Prediction of Gut Microbiota in Pigeon

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