常见SPF级小鼠和大鼠肠道菌群多样性研究
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摘要
目的研究常见SPF级小鼠和大鼠的肠道菌群多样性。方法分别采集广东地区三家实验动物生产单位的C57BL/6、ICR、BALB/c小鼠和Wistar、SD大鼠的盲肠内容物样品,用细菌16S rDNA通用引物扩增V4-V5区域,采用Illumina Miseq 2×300 bp测序平台进行测序,使用生物信息学方法进行微生物群落分析、Alpha多样性分析与Beta多样性分析。结果对序列去杂优化后OTU聚类分析,稀释性曲线说明本次测序的数据量合理;实验小鼠和大鼠肠道菌群共分成八个门,其中拟杆菌门(Bacteroidetes)、厚壁菌门(Firmicutes)占据主要地位,属水平上主要是拟杆菌属(Bacteroides)、Hungatella、副杆状菌属(Parabacteroides)、乳酸杆菌属(Lactobacillus)等;样品间差异性分析显示相同设施来源动物的菌群组成相似性较高;Alpha分析结果显示来源于同种设施的动物物种丰富度相近;Beta分析显示相同设施动物的肠道菌群差异较小,但品系对肠道菌群差异性有所影响。结论不同来源设施的饲养环境是动物肠道菌群多样性的主要影响因素,不同品系对肠道菌群多样性有一定影响。
Objective To study the diversity of intestinal flora in commonly used SPF mice and rats. Methods The cecum contents of C57 BL/6, ICR, BALB/c mice as well as Wistar and SD rats were collected from three experimental animal production units in the Guangdong area. The V4-V5 region was amplified using 16 S rDNA primers and sequenced by the Illumina Miseq 2 x 300 bp sequencing platform. Microbial community analysis, alpha diversity analysis, and beta diversity analysis were carried out by bioinformatics. Results In OTU cluster analysis after sequence removal optimization, the dilution curve indicated that the data quantity of the sequencing was reasonable. The intestinal microflora of mice and rats were divided into eight phyla. Bacteroidetes and Firmicute phyla occupied the main position, mainly in the level of Bacteroides, followed by the genuses Hungatella and Parabacteroides and then Lactobacillus. Analysis of the differences among the samples showed that the flora composition of animals from the same facility, and that of the same strains from the same facility was also similar. Alpha analysis showed that the species richness was similar in animals from the same facility, and beta analysis showed little difference in intestinal flora of the same origin animals. Moreover, the strain had an effect on the difference of intestinal flora. Conclusions The origin is the main factor influencing the diversity of intestinal flora, and the strain has a certain influence on their diversity.
Objective To study the diversity of intestinal flora in commonly used SPF mice and rats. Methods The cecum contents of C57 BL/6, ICR, BALB/c mice as well as Wistar and SD rats were collected from three experimental animal production units in the Guangdong area. The V4-V5 region was amplified using 16 S rDNA primers and sequenced by the Illumina Miseq 2 x 300 bp sequencing platform. Microbial community analysis, alpha diversity analysis, and beta diversity analysis were carried out by bioinformatics. Results In OTU cluster analysis after sequence removal optimization, the dilution curve indicated that the data quantity of the sequencing was reasonable. The intestinal microflora of mice and rats were divided into eight phyla. Bacteroidetes and Firmicute phyla occupied the main position, mainly in the level of Bacteroides, followed by the genuses Hungatella and Parabacteroides and then Lactobacillus. Analysis of the differences among the samples showed that the flora composition of animals from the same facility, and that of the same strains from the same facility was also similar. Alpha analysis showed that the species richness was similar in animals from the same facility, and beta analysis showed little difference in intestinal flora of the same origin animals. Moreover, the strain had an effect on the difference of intestinal flora. Conclusions The origin is the main factor influencing the diversity of intestinal flora, and the strain has a certain influence on their diversity.
引文
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[9] Eckburg PB,Bik EM,Bernstein CN,et al.Diversity of the human intestinal microbial flora [J].Science,2005,308(5728):1635-1638.
[10] 李伟.几种常用实验动物与人肠道主要菌群多样性比较 [D].重庆:西南大学,2011.Li W.Comparison of the diversity of the faecal microbiota among laboratory mouse,rat,miniature pig and human [D].Chongqing:Southwest University,2011.
[11] Qin J,Li R,Raes J,et al.A human gut microbial gene catalogue established by metagenomic sequencing [J].Nature,2010,464(7285):59-65.
[12] 郭玉倩,角建林,袁鑫,等.树鼩大肠内容物细菌的群落多样性分析[J].中国比较医学杂志,2018,28(9):7-13+32.Guo YQ,Jiao JL,Yuan X,et al.Diversity analysis of the tree shrew hindgut microbiota by Illumina PE250 sequencing technology [J].Chin J Comp Med,2018,28(9):7-13+32.
[2] Ley RE,Peterson DA,Gordon JI.Ecological and evolutionary forces shaping microbial diversity in the human intestine [J].Cell,2006,124:837-848.
[3] 叶玉江.中国实验动物资源调查与发展趋势[M].北京:科学出版社,2017:101-105.Ye YJ.Investigation and Development trend of Laboratory Animal Resources in China [M].Beijing:Science Press,2017:101-105.
[4] 林璋,祖先鹏,谢海胜,等.肠道菌群与人体疾病发病机制的研究进展[J].药学学报,2016,51 (6):843-852.Lin Z,Zu XP,Xie HS,et al.Research progress in mechanism of intestinal microorganisms in human diseases [J].Acta Pharm Sin,2016,51(6):843-852.
[5] 郭慧玲,邵玉宇,孟和毕力格,等.肠道菌群与疾病关系的研究进展[J].微生物学通报,2015,42(2):400-410.Guo HL,Shao YY,Meng HBLG,et al.Research on the relation between gastrointesinal microbiota and disease [J].Microbiol Chin,2015,42(2):400-410.
[6] 谷莉.不同鼠种的肠道菌群在不同饮食结构干预中的组成改变[D].长沙:中南大学,2014.Gu L.The effect of of different diet on intestinal flora composition in different rat species[D].Changsha:Central South University,2014.
[7] 杨永华,姚健.分子生物学方法在微生物多样性研究中的应用[J].生物多样性,2000,8(3):337-342.Yang YH,Yao J.Molecular techniques and their application to the study of microbial diversity [J].Biodiv Sci,2000,8(3):337-342.
[8] 范薇.实验小鼠肠道正常菌群[J].中国比较医学杂志,2004,14(1):58-60.Fan W.Normal Intestinal Microflora of Mice [J].Chin J Comp Med,2004,14(1):58-60.
[9] Eckburg PB,Bik EM,Bernstein CN,et al.Diversity of the human intestinal microbial flora [J].Science,2005,308(5728):1635-1638.
[10] 李伟.几种常用实验动物与人肠道主要菌群多样性比较 [D].重庆:西南大学,2011.Li W.Comparison of the diversity of the faecal microbiota among laboratory mouse,rat,miniature pig and human [D].Chongqing:Southwest University,2011.
[11] Qin J,Li R,Raes J,et al.A human gut microbial gene catalogue established by metagenomic sequencing [J].Nature,2010,464(7285):59-65.
[12] 郭玉倩,角建林,袁鑫,等.树鼩大肠内容物细菌的群落多样性分析[J].中国比较医学杂志,2018,28(9):7-13+32.Guo YQ,Jiao JL,Yuan X,et al.Diversity analysis of the tree shrew hindgut microbiota by Illumina PE250 sequencing technology [J].Chin J Comp Med,2018,28(9):7-13+32.