ANALYSIS OF INTESTINAL MICROORGANISMS IN TRIPLOPHYSA ROSA (TELEOSTEI, CYPRINIFORMES)
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摘要: 研究旨在分析玫瑰高原鳅(Triplophysa rosa)肠道微生物的结构组成和多样性, 探索其肠道微生物的潜在功能。提取了5尾玫瑰高原鳅的肠道总DNA, 运用Illumina Miseq平台对肠道微生物16S rRNA的V3—V4区进行了测序, 统计样品肠道微生物的操作分类单元(Operational Taxonomic Units, OTUs)数量, 分析物种组成、丰度及Alpha多样性, 并预测肠道微生物的功能。结果显示, 玫瑰高原鳅的肠道微生物有19门、31纲、87目、 146科、253属、 320种, 451个OTUs。在门水平上, 优势菌群为变形菌门(Proteobacteria)、放线菌门(Actinobacteria)和拟杆菌门(Bacteroidetes); 在属水平上, 优势菌群为气单胞菌属(Aeromonas)、爱德华菌属(Edwardsiella)、邻单胞菌属(Plesiomonas)和希瓦氏菌属(Shewanella)。功能预测表明, 肠道微生物编码的大多数基因与新陈代谢相关, 其中“碳水化合物运输和代谢”和“氨基酸转运与代谢”功能类群的相对丰度较高。玫瑰高原鳅肠道内微生物组成复杂, 其功能分析有助于理解肠道微生物对玫瑰高原鳅摄食的影响, 为进一步研究玫瑰高原鳅的食性提供了理论基础。Abstract: Triplophysa rosa is a typical cave-dwelling fish distributed at Wulong County, Chongqing, China. It has degenerated eyes, albino skin, and highly developed sense organs, but its gut microbial function adapted to cave remains to be settled. The aims of this study were to analyze the structure and diversity of intestinal microorganisms in T. rosa and to explore the function of intestinal microorganisms. We extracted total intestinal DNA of 5 T. rosa, and then sequenced the V3—V4 region of 16S rRNA using Illumina Miseq sequencing technology. The number of operational taxonomic units (OTUs) of intestinal microorganisms was counted to analyze species composition, abundance, and Alpha diversity. The function of intestinal microorganisms was predicted by PICRUSt. A total of 451 OTUs of the high-quality sequences were obtained, belonging to 19 phyla, 31 classes, 87 orders, 146 families, 253 genera, and 320 species. At the phylum level, Proteobacteria, Actinobacteria, and Bacteroidetes were the dominant microorganisms. At the genus level, Aeromonas, Edwardsiella, Plesiomonas, and Shewanella were the main microorganisms. Functional prediction showed that most of the genes encoded by intestinal microorganisms are related to metabolism with the highest relationship with “amino acid transport and metabolism” and “carbohydrate transport and metabolism”. The composition of the microorganisms in the intestinal tract of T. rosa is complex, and functional analysis is helpful to understand the influence of intestinal microorganisms on its feeding, providing a theoretical basis for further study on fish diet.
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Keywords:
- Triplophysa rosa /
- Intestinal microorganisms /
- 16S rRNA /
- Diversity /
- Function
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图 2 各样本OTUs的韦恩图
图中数字表示5个样本中共有的和独有的OTU数量
Figure 2. The venn diagram of each sample’s OTUs
The number of common and unique OTU in 5 samples
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图 3 基于门水平的玫瑰高原鳅肠道菌群结构
Proteobacteria. 变形菌门; Unclassified. 未鉴定; Actinobacteria. 放线菌门; Bacteroidetes. 拟杆菌门; Firmicutes. 厚壁菌门; Others. 其他丰度小于1%的菌群之和
Figure 3. Bacterial structure evaluated at the phylum taxonomical level in T. rosa
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图 4 基于属水平的玫瑰高原鳅肠道菌群结构
Aeromonas. 气单胞菌属; Edwardsiella. 爱德华菌属; Plesiomonas. 邻单胞菌属; Shewanella. 希瓦氏菌属; Vibrio. 弧菌属; Unclassified. 未鉴定; Pseudomonas. 假单胞菌属; Paenarthrobacter; Flavobacterium. 黄杆菌属; Ralstonia. 罗尔斯通菌属; Acinetobacter. 不动杆菌属; Bacillus. 芽孢杆菌属; Others. 其他
Figure 4. Bacterial structure evaluated at the genus taxonomical level in T. rosa
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图 5 玫瑰高原鳅肠道微生物的COG功能分类统计
A. RNA处理和修饰RNA processing and modification; B. 染色质结构与动力学Chromatin structure and dynamics; C. 能源生产与转化Energy production and conversion; D. 细胞周期控制、细胞分裂、染色体分裂Cell cycle control, cell division, chromosome partitioning; E. 氨基酸转运与代谢Amino acid transport and metabolism; F. 核苷酸的转运和代谢Nucleotide transport and metabolism; G. 碳水化合物运输和代谢Carbohydrate transport and metabolism; H. 辅酶运输和代谢Coenzyme transport and metabolism; I. 脂质转运与代谢Lipid transport and metabolism; J. 翻译、核糖体结构和生物发生Translation, ribosomal structure and biogenesis; K. 转录终止Transcription termination; L. 复制、重组和修复Replication, recombination and repair; M. 细胞壁/膜/信封生源论Cell wall/membrane/envelope biogenesis; N. 细胞运动Cell motility; O. 翻译后修饰、蛋白质周转、伴侣Posttranslational modification, protein turnover, chaperones; P. 无机离子运输与代谢Inorganic ion transport and metabolism; Q. 次生代谢产物的合成、运输和分解代谢Secondary metabolites biosynthesis, transport and catabolism; R. 一般功能预测General function prediction only; S. 功能未知Function unknown; T. 信号转导机制Signal transduction mechanisms; U. 细胞内运输、分泌和囊泡运输Intracellular trafficking, secretion, and vesicular transport; V. 防御机制Defense mechanisms; W. 真核细胞的细胞外结构Extracellular structures; Y. 核结构Nuclear structure; Z. 细胞骨架Cytoskeleton
Figure 5. The COG function classification of intestinal microorganisms in T. rosa
表 1 Alpha多样性统计
Table 1 The statistics of Alpha-diversity
样本编号Sample number 香农指数Shannon index 辛普森指数Simpson index ACE指数ACE index Chao1 指数Chao1 index 覆盖率Coverage TR1 0.823 0.725 115.433 121.100 0.999 TR2 1.505 0.626 268.554 272.875 1.000 TR3 1.169 0.478 124.584 89.750 0.999 TR4 0.868 0.668 184.968 186.000 0.998 TR5 0.325 0.919 208.514 198.232 0.999 注: TR为玫瑰高原鳅拉丁文名的缩写, 其后的数字表示样本编号Note: TR. Triplophysa rosa, the number behind TR means sample number 
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表 2 KEGG代谢通路统计
Table 2 Metabolic pathway statistics based on KEGG
编号Number 功能Function 丰度Abundance 1 新陈代谢Metabolism 45059885 2 环境信息处理Environmental information processing 17740636 3 遗传信息处理Genetic information processing 15714193 4 细胞进程Cellular processes 5518399 5 人类疾病;Human diseases 1146337 6 有机系统Organismal systems 672877 7 无None 195855
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