树鼩肠道菌群多样性与功能预测研究
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摘要
[目的]鉴定树鼩的肠道菌群,分析树鼩肠道菌群多样性和丰度,并进行菌群功能预测。[方法]随机采集3份雄性树鼩粪便样品,提取树鼩粪便中细菌基因组DNA,通过PCR扩增获得16S rRNA V3～V4片段,采用高通量Illumina PE300平台进行测序,利用BIPES以及QIIME分析并比较菌群结构及多样性。最后,通过PICRUS t软件对肠道菌群的功能进行预测。[结果]树鼩肠道粪便细菌有9门20纲33目53属122种208个OTU。门水平上,优势菌群为厚壁菌门(Firmicutes)和变形菌门(Proteobacteria);属水平上,埃希氏杆菌属(Escherichia)、乳酸菌属(Lactobacillus)和肠球菌属(Enterocossus)为优势菌群。PICRUS t功能预测结果表明,肠道细菌编码的大多数基因与代谢相关,其次是基因信息加工、环境信息加工。COG功能分类分析表明肠道微生物基因在"氨基酸的运输和代谢"和"碳水化合物运输与代谢"功能类群的相对丰度较高。[结论]PICRUS t功能预测到树鼩肠道菌群主要与代谢相关,树鼩肠道菌群是研究肠道菌群与代谢类疾病的一种良好试验材料。
[Objective]To identify the intestinal flora of Tupaia belangeri,analyze the diversity and abundance,and predict the function of the flora.[Method]Three male feces samples of T.belangeri were randomly collected,bacterial genomic DNA were extracted from the feces samples of T.belangeri to make PCR amplification.16 S rRNA V3-V4 fragments were obtained.The high-throughput Illumina PE300 platform was used for sequencing,and the structure and diversity of the bacterial flora were analyzed by BIPES and QIIME.The function of intestinal flora was predicted through PICRUS t.[Result]There were 9 phyla,20 phyla,33 orders,53 genera,122 species,208 OTU in the intestinal fecal flora of T.belangeri.Firmicutes and Proteobacteria dominated at the level of phylum.At the level of genus,Escherichia,Lactobacillus and Enterocossus were the dominant flora.The functional prediction results by PICRUS t showed that most genes encoded by gut bacteria were associated with metabolic "metabolism",followed by genetic information processing "based information processing",environmental information processing "environmental information processing".COG gene function classification statistics showed that the relative abundance of intestinal flora in "amino acid transport and metabolism" and "carbohydrate transport and metabolism" were higher.[Conclusion]The function of PICRUS t predicted that the intestinal flora of T.belangeri was mainly related with the metabolism,and the intestinal flora of T.belangeri was a good experimental material for studying intestinal flora and metabolic diseases.
[Objective]To identify the intestinal flora of Tupaia belangeri,analyze the diversity and abundance,and predict the function of the flora.[Method]Three male feces samples of T.belangeri were randomly collected,bacterial genomic DNA were extracted from the feces samples of T.belangeri to make PCR amplification.16 S rRNA V3-V4 fragments were obtained.The high-throughput Illumina PE300 platform was used for sequencing,and the structure and diversity of the bacterial flora were analyzed by BIPES and QIIME.The function of intestinal flora was predicted through PICRUS t.[Result]There were 9 phyla,20 phyla,33 orders,53 genera,122 species,208 OTU in the intestinal fecal flora of T.belangeri.Firmicutes and Proteobacteria dominated at the level of phylum.At the level of genus,Escherichia,Lactobacillus and Enterocossus were the dominant flora.The functional prediction results by PICRUS t showed that most genes encoded by gut bacteria were associated with metabolic "metabolism",followed by genetic information processing "based information processing",environmental information processing "environmental information processing".COG gene function classification statistics showed that the relative abundance of intestinal flora in "amino acid transport and metabolism" and "carbohydrate transport and metabolism" were higher.[Conclusion]The function of PICRUS t predicted that the intestinal flora of T.belangeri was mainly related with the metabolism,and the intestinal flora of T.belangeri was a good experimental material for studying intestinal flora and metabolic diseases.
引文
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[11]张芹,周中凯,任晓冲,等.高通量测序技术研究糖尿病大鼠与正常大鼠粪便菌群的结构差异[J].中国食品学报,2017,17(6):232-238.
[12]MORGAN X C,TICKLE T L,SOKOL H,et al.Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment[J].Genome Biol,2012,13(9):1-18.
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[16]HOOPER L V,MACPHERSON A J.Immune adaptations that maintain homeostasis with the intestinal microbiota[J].Nat Rev Immunol,2010,10(3):159-169.
[17]RUIZ L,MARGOLLES A,SNCHEZ B.Bile resistance mechanisms in Lactobacillus and Bifidobacterium[J].Frontiers in microbiology,2013,4:396.
[2]LI R F,YUAN B,XIA X S,et al.Tree shrew as a new animal model to study the pathogenesis of avian influenza(H9N2)virus infection[J].E-merging microbes&infections,2018,7(166):1-11.
[3]黄晓燕,徐娟,孙晓梅,等.树鼩在人类疾病动物模型中应用研究进展[J].实验动物科学,2013,30(2):59-64.
[4]刘昌孝.肠道菌群与健康、疾病和药物作用的影响[J].中国抗生素杂志,2018,43(1):1-12.
[5]BEYO GˇLU D,SMITH R L,IDLE J R.Dog bites man or man bites dog?The enigma of the amino acid conjugations[J].Biochem pharmacol,2012,83(10):1331-1339.
[6]UMESAKI Y,SETOYAMA H.Structure of the intestinal flora responsible for development of the gut immune system in a rodent model[J].Microbes Infect,2000,2(11):1343-1351.
[7]沈男,刘毅,盖中涛.肠道菌群与肠道疾病关系的研究进展[J].基础医学与临床,2018,38(7):1034-1037.
[8]CAPORASOA J G,LAUBERB C L,WALTERS W A,et al.Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample[J].PANS,2011,108(S1):4516-4522.
[9]QUSAT C,PRUESSE E,YILMAZ P,et al.The SILVA ribosomal RNA gene dataset project:Improved data processing and web-based tools[J].Nucl Acids Res,2013,41:590-596.
[10]杨俊花,赵志辉,郭文博,等.应用Illumina-Mi Seq高通量测序技术分析脱氧雪腐镰刀菌烯醇对小鼠肠道菌群的影响[J].动物营养学报,2017,29(1):158-167.
[11]张芹,周中凯,任晓冲,等.高通量测序技术研究糖尿病大鼠与正常大鼠粪便菌群的结构差异[J].中国食品学报,2017,17(6):232-238.
[12]MORGAN X C,TICKLE T L,SOKOL H,et al.Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment[J].Genome Biol,2012,13(9):1-18.
[13]LANGILLE M G,ZANEVELD J,CAPORASO J G,et al.Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences[J].Nature biotechnology,2013,31(9):814-821.
[14]LEY R E,TURNBAUGH P J,KLEIN S,et al.Microbial ecology:Human gut microbes associated with obesity[J].Nature,2006,444:1022-1023.
[15]LEY R E,PETERSON D A,GORDON J I.Ecological and evolutionary forces shaping microbial diversity in the human intestine[J].Cell,2006,124(4):837-848.
[16]HOOPER L V,MACPHERSON A J.Immune adaptations that maintain homeostasis with the intestinal microbiota[J].Nat Rev Immunol,2010,10(3):159-169.
[17]RUIZ L,MARGOLLES A,SNCHEZ B.Bile resistance mechanisms in Lactobacillus and Bifidobacterium[J].Frontiers in microbiology,2013,4:396.