不同养殖场林麝肠道微生物组成和功能的差异

doi:10.16829/j.slxb.150701

兽类学报 ›› 2023, Vol. 43 ›› Issue (2): 129-140.DOI: 10.16829/j.slxb.150701

• 研究论文 • 下一篇

不同养殖场林麝肠道微生物组成和功能的差异

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()

^1.中国科学院西北高原生物研究所，高原生物适应与进化重点实验室，西宁 810001
^2.中国科学院大学，北京 100049
^3.青海省动物生态基因组学重点实验室，西宁 810001

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:
中国科学院战略性先导科技专项(XDA23060602);青海省重点研发与转化计划(2019-SF-150);中国科学院-青海省人民政府三江源国家公园联合研究专项(LHZX-2020-01)

Comparative analysis of gut microbial composition and functions of forest musk deer in different breeding centres

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()

^1.Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810001, China
^2.University of Chinese Academy of Sciences, Beijing 100049, China
^3.Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Xining 810001, China

Received:2022-06-06 Accepted:2022-10-20 Online:2023-03-30 Published:2023-03-23
Contact: Tongzuo ZHANG

摘要/Abstract

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。

关键词: 林麝, 肠道微生物, 功能, 多样性, 16S rRNA基因测序

Abstract:

Intestinal diseases are common in the breeding of forest musk deer (Moschus berezovskii, FMD). Gut microbiota has evolved with the host and formed a complex microecosystem with the gastrointestinal tract of animals. To compare the effects of different breeding environments on gut microbial composition and functions of captive FMD, a total of 215 fresh feces samples were collected from 5 different breeding centres in China, and a 16S rRNA gene high-throughput sequencing was performed. The differences in gut microbial composition, diversity, and functions of FMD from different breeding centres were analyzed. The results showed that Firmicutes and Bacteroides were the absolute dominant bacteria phyla in the gut microbiota of FMD fed without compound probiotics from Qilian County, while Firmicutes and Proteobacteria were the absolute dominant bacteria in the gut microbiota of FMD fed with compound probiotics from Liangdang County and Feng County. The composition, dominant bacteria phyla, dominant bacteria genera, potential pathogenic bacteria, metabolism-related, and disease-related functions of gut microbiota in FMD from different breeding centres were significantly different. The α diversity and disease-related function enrichment of gut microbiota in FMD from Qilian were significantly lower than those from other breeding centres, and enterotype 2 was dominant, with Firmicutes, UCG-005,and Bacteroides as the marker bacteria. The relative abundance of potential pathogenic bacteria of gut microbiota in FMD from Liangdang and Feng Counties was low. We speculated that the difference in food composition might be the main factor leading to the difference in the gut microbiota of FMD from different breeding centres, and the use of compound probiotics might be an important factor leading to the decrease of α diversity and potential pathogenic bacteria. The results of this study can provide a scientific basis for the artificial breeding management of FMD, and also have certain significance for the assessment of the artificial breeding environment and the plan of reintroduction in the future.

Key words: Forest musk deer, Gut microbiota, Functions, Diversity, 16S rRNA gene sequencing

中图分类号:

Q938

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/表 6

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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不同养殖场林麝肠道微生物组成和功能的差异

Comparative analysis of gut microbial composition and functions of forest musk deer in different breeding centres

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