兽类学报 ›› 2023, Vol. 43 ›› Issue (2): 129-140.DOI: 10.16829/j.slxb.150701
• 研究论文 • 下一篇
江峰1,3(), 宋鹏飞1,2,3, 张婧捷1,2,3, 高红梅1,3, 汪海静1,2,3, 蔡振媛1,3, 刘道鑫1,2,3, 张同作1,3()
收稿日期:
2022-06-06
接受日期:
2022-10-20
出版日期:
2023-03-30
发布日期:
2023-03-23
通讯作者:
张同作
作者简介:
江峰 (1992- ),男,博士,主要从事动物生态学、保护生物学研究. E-mail: jiangfeng@nwipb.cas.cn
基金资助:
Feng JIANG1,3(), Pengfei SONG1,2,3, Jingjie ZHANG1,2,3, Hongmei GAO1,3, Haijing WANG1,2,3, Zhenyuan CAI1,3, Daoxin LIU1,2,3, Tongzuo ZHANG1,3()
Received:
2022-06-06
Accepted:
2022-10-20
Online:
2023-03-30
Published:
2023-03-23
Contact:
Tongzuo ZHANG
摘要:
肠道疾病是养殖林麝 (Moschus berezovskii) 常见疾病。动物肠道微生物伴随宿主进化并与胃肠道构成了复杂的微生态系统。为探究不同饲养环境对圈养林麝肠道微生物组成和功能的影响,本研究对采自国内5个不同养殖场的215份粪便样品进行了16S rRNA基因高通量测序,对比分析不同养殖场林麝肠道微生物组成、多样性和功能的差异。结果显示,厚壁菌门和拟杆菌门是未喂食复合益生菌的祁连县养殖场林麝肠道菌群的绝对优势菌门,而喂食复合益生菌的甘肃两当县和陕西凤县的4家养殖场林麝肠道菌群的绝对优势菌门为厚壁菌门和变形菌门。不同养殖场林麝肠道菌群组成、优势菌门、优势菌属、潜在致病菌、代谢及疾病相关功能均有显著差异。祁连县养殖场林麝肠道微生物的α多样性和疾病相关功能表达量显著低于其他养殖场,并以肠型2为主,其主导菌为厚壁菌门、UCG-005和拟杆菌属;两当县和凤县的4家养殖场林麝肠道菌群潜在致病菌相对丰度较低。本研究推测食物组成差异可能是导致不同养殖场林麝肠道微生物差异的主要因素,复合益生菌的使用可能是导致α多样性和潜在致病菌下降的重要因素。该结果可为林麝的人工养殖和有效管理提供科学依据,也对人工饲养环境评估和未来的再引入计划具有一定指导意义。
中图分类号:
江峰, 宋鹏飞, 张婧捷, 高红梅, 汪海静, 蔡振媛, 刘道鑫, 张同作. 不同养殖场林麝肠道微生物组成和功能的差异[J]. 兽类学报, 2023, 43(2): 129-140.
Feng JIANG, Pengfei SONG, Jingjie ZHANG, Hongmei GAO, Haijing WANG, Zhenyuan CAI, Daoxin LIU, Tongzuo ZHANG. Comparative analysis of gut microbial composition and functions of forest musk deer in different breeding centres[J]. ACTA THERIOLOGICA SINICA, 2023, 43(2): 129-140.
图1 不同养殖场林麝肠道微生物组成分析. A:基于Sobs指数的测序样本稀释曲线;B:门相对丰度柱状图,红色字体表示优势菌门;C:可鉴别细菌属 (Top 70) 聚类热图分析,红色、蓝色、黑色、橙色和绿色文字分别表示厚壁菌门、拟杆菌门、变形菌门、放线菌门和浮霉菌门的细菌属;D:门和属水平Venn图分析. QL:祁连县养殖场;LD:两当县养殖场;FX:凤县养殖场;FR:散养场. 以下图中注释相同
Fig. 1 Analyses of gut microbial composition of forest musk deers (FMD) in different breeding centres. A: Rarefaction curves based on Sobs; B: Relative abundance of bacterial phyla. The dominant phyla were shown in red; C: Cluster heat map analysis of identifiable bacterial genera (Top 70), the red, blue, black, orange and green text indicated Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria and Planctomycetes, respectively. D: Venn diagrams at phylum and genus level. QL: Farm in Qilian County; LD: Farm in Liangdang County; FX: Farm in Feng County; FR:Free-range farm. Same notes in the following figure
图2 不同养殖场林麝肠道微生物多样性分析. Sobs (A)、Shannon (B)、Chao1 (C) 和 PD (D) 指数的α多样性组间差异分析;不同养殖场林麝肠道菌群组间PCoA聚类分析 (E) 和NMDS聚类分析 (F). *P < 0.05 (Wilcoxon rank-sum test),**P < 0.01,***P < 0.001
Fig. 2 Analyses of gut microbial diversity of forest musk deers in different breeding centres. Analysis of differences in α diversity between groups based on Sobs (A), Shannon (B), Chao1 (C) and PD (D) indices. PCoA analysis (E) and NMDS analysis (F) among different farms. *P < 0.05 (Wilcoxon rank-sum test), **P < 0.01, ***P < 0.001
图3 不同养殖场林麝肠道菌群优势菌组间差异分析. 优势菌门组间差异分析 (A);厚壁菌门 (B)、变形菌门 (C)、拟杆菌门 (D) 和放线菌门 (E) 中优势菌属组间差异分析. ***P < 0.001 (Kruskal-Wallis test)
Fig. 3 Differences of dominant bacteria in gut microbiota of forest musk deers in different breeding centres. Analysis of the differences between the dominant phyla (A); Analysis of the differences between the dominant genera belonging to Firmicutes (B), Proteobacteria (C), Bacteroidetes (D), Actinobacteria (E). ***P < 0.001 (Kruskal-Wallis test)
图4 基于KEGG数据库 (A) 和eggNOG数据库 (B) 的功能注释及level 2水平上代谢功能的组间差异分析. *P < 0.05 (Wilcoxon rank-sum test),**P < 0.01,***P < 0.001. ns,不显著
Fig. 4 Functional annotation based on KEGG database (A) and eggNOG database (B), and analysis of the differences of metabolic functions between groups at the level-2 level. **P < 0.01, ***P < 0.001. ns, not significant
图5 不同养殖场林麝肠道菌群中潜在致病菌 (A) 与疾病相关功能富集 (B) 组间差异分析. *P < 0.05,**P < 0.01,***P < 0.001,ns,无显著差异
Fig. 5 Analysis of the differences of potential pathogenic bacteria (A) and disease related functions (B) of forest musk deers in different breeding centres. *P < 0.05, **P < 0.01, ***P < 0.001. ns, not significant
图6 不同养殖场林麝肠型差异分析. A:最优集群数分析和肠型分型图分析;B:不同养殖场林麝肠道菌群肠型分布分析;C:不同肠型α多样性差异性分析;D:门水平和属水平上不同肠型LEfSe分析;E:不同肠型生物标记物 (biomarker) 组间差异分析
Fig. 6 Analysis of different enterotype in forest musk deers from different breeding centres. A: Analysis of optimal cluster number and enterotype map; B: Distribution of enterotype in different farms; C: Analysis of α diversity in different enterotypes; D: LEfSe analysis of different enterotypes at phylum and genus levels; E: Difference analysis of biomarkers of different enterotypes
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