利用Illumina测序技术分析圈养成年滇金丝猴肠道菌群多样性
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摘要
选取中国科学院昆明灵长类研究中心的4只成年健康滇金丝猴和1只成年亚健康滇金丝猴,基于高通量测序技术分析其肠道细菌群落的组成和多样性,探讨健康状况对成年滇金丝猴肠道微生物的影响,揭示其肠道微生态特征。结果表明:在门水平上,健康滇金丝猴的主要菌群有厚壁菌门(Firmicutes,78. 41%)、拟杆菌门(Bacteroidetes,18. 97%);在属水平上,主要菌群有瘤胃球菌属(Ruminococcus,6. 29%)、未分类的毛螺菌科(unidentified Lachnospiraceae,4. 20%)成员、普氏菌属(Prevotella,3. 24%)。亚健康滇金丝猴肠道菌群中螺旋体门(Spirochaetes,6. 09%)和变形菌门(Proteobacteria,3. 09%)的含量显著高于健康滇金丝猴(Spirochaetes 0. 14%; Proteobacteria 1. 32%)的含量。
We investigated the composition and diversity of the intestinal bacterial community and the effects on health of four adult snub-nosed monkeys( Rhinopithecus bieti). Three monkeys were healthy and one showed signs of illness. All four monkeys came from Kunming Primate Research Center,CAS. We studied intestinal bacteria by use of high-throughput sequencing technology. At phylum level,the main flora of healthy monkeys were Firmicutes( 78. 41%) and Bacteroidetes( 18. 97%). At genus level,the main bacterial groups were Ruminococcus( 6. 29%),members of unidentified Lachnospiraceae( 4. 20%),and Prevotella( 3. 24%). The contents of Spirochaetes( 6. 09%) and Proteobacteria( 3. 09%) in the intestinal flora of sub-healthy monkeys were significantly greater than in healthy monkeys( Spirochaetes 0. 14%, and Proteobacteria1. 32%).
We investigated the composition and diversity of the intestinal bacterial community and the effects on health of four adult snub-nosed monkeys( Rhinopithecus bieti). Three monkeys were healthy and one showed signs of illness. All four monkeys came from Kunming Primate Research Center,CAS. We studied intestinal bacteria by use of high-throughput sequencing technology. At phylum level,the main flora of healthy monkeys were Firmicutes( 78. 41%) and Bacteroidetes( 18. 97%). At genus level,the main bacterial groups were Ruminococcus( 6. 29%),members of unidentified Lachnospiraceae( 4. 20%),and Prevotella( 3. 24%). The contents of Spirochaetes( 6. 09%) and Proteobacteria( 3. 09%) in the intestinal flora of sub-healthy monkeys were significantly greater than in healthy monkeys( Spirochaetes 0. 14%, and Proteobacteria1. 32%).
引文
[1] 丁赟,吴琦,胡义波,等.野生哺乳动物肠道微生物组研究进展与展望[J].兽类学报,2017,37(4):399-406.
[2] BENGMARK S.Gut microbiota,immune development and function[J].Pharmacological Research,2013,69(1):87-113.
[3] YILDIRIM S,YEOMAN C J,SIPOS M,et al.Characterization of the fecal microbiome from non-human wild primates reveals species specific microbial communities[J].PLoS One,2010,5(11):e13963.
[4] 赵娜,刘社兰,路纪琪,等.中国恒河猴肠道菌群特征揭示[J].生物技术通报,2013,29(7):153-160.
[5] 姚丽娟.不同年龄段神农架金丝猴肠道菌群组成和差异的研究[D].武汉:华中农业大学,2015.
[6] 王剑.健康和腹泻成年川金丝猴粪样菌群比较分析[D].雅安:四川农业大学,2015.
[7] GRIFFIN N W,AHERN P P,CHENG J Y,et al.Prior dietary practices and connections to a human gut microbial metacommunity alter responses to diet interventions[J].Cell Host & Microbe,2017,21(1):84-96.
[8] UENISHI G,FUJITA S,OHASHI G,et al.Molecular analyses of the intestinal microbiota of chimpanzees in the wild and in captivity[J].American Journal of Primatology,2007,69(4):367-376.
[9] BIAGI E,NYLUND L,CANDELA M,et al.Through ageing,and beyond:gut microbiota and inflammatory status in seniors and centenarians[J].PLoS One,2010,5(5):e10667.
[10] COSTELLO E K,GORDON J I,SECOR S M,et al.Postprandial remodeling of the gut microbiota in Burmese pythons[J].The ISME Journal,2010,4(11):1375-1385.
[11] ISMAIL N A,RAGAB S H,ELBAKY A A,et al.Frequency of firmicutes and bacteroidetes in gut microbiota in obese and normal weight Egyptian children and adults[J].Archives of Medical Science,2011,7(3):501-507.
[12] 简平,王强,王剑,等.不同年龄段川金丝猴肠道菌群结构差异分析[J].动物营养学报,2015,27(4):1302-1309.
[13] JEWELL K A,SCOTT J J,ADAMS S M,et al.A phylogenetic analysis of the phylum Fibrobacteres[J].Systematic and Applied Microbiology,2013,36(6):376-382.
[14] ZHOU X M,WANG B S,PAN Q,et al.Whole-genome sequencing of the snub-nosed monkey provides insights into folivory and evolutionary history[J].Nature Genetics,2014,46(12):1303-1310.
[15] WANG Y H,HUANG Y.Effect of Lactobacillus acidophilus and Bifidobacterium bifidum supplementation to standard triple therapy on Helicobacter pylori eradication and dynamic changes in intestinal flora[J].World Journal of Microbiology and Biotechnology,2014,30(3):847-853.
[16] TROTT D J,MCLAREN A J,HAMPSON D J.Pathogenicity of human and porcine intestinal spirochetes in one-day-old specific-pathogen-free chicks:an animal model of intestinal spirochetosis[J].Infection and Immunity,1995,63(9):3705-3710.
[17] ARUMUGAM M,RAES J,PELLETIER E,et al.Enterotypes of the human gut microbiome[J].Nature,2011,473(7346):174-180.
[18] SHINKAI T,UEKI T,KOBAYASHI Y.Detection and identification of rumen bacteria constituting a fibrolytic consortium dominated by Fibrobacter succinogenes[J].Animal Science Journal,2010,81(1):72-79.
[19] BIAN G R,MA L,SU Y,et al.The microbial community in the feces of the white rhinoceros(Ceratotherium simum)as determined by barcoded pyrosequencing analysis[J].PLoS One,2013,8(7):e70103.
[20] DALY K,PROUDMAN C J,DUNCAN S H,et al.Alterations in microbiota and fermentation products in equine large intestine in response to dietary variation and intestinal disease[J].British Journal of Nutrition,2012,107(7):989-995.
[21] CARLIER J P,BEDORA-FAURE M,K'OUAS G,et al.Proposal to unify Clostridium orbiscindens Winter et al.1991 and Eubacterium plautii(Séguin 1928)Hofstad and Aasjord 1982,with description of Flavonifractor plautii gen.nov.,comb.nov.,and reassignment of Bacteroides capillosus to Pseudoflavonifractor capillosus gen.nov.,comb.nov.[J].International Journal of Systematic and Evolutionary Microbiology,2010,60(3):585-590.
[22] MASLOWSKI K M,MACKAY C R.Diet,gut microbiota and immune responses[J].Nature Immunology,2011,12(1):5-9.
[23] EDITOR T.Microbes in your gut could be cause of allergies[J].Emerging Infectious Diseases.
[24] LI M,GU D,XU N,et al.Gut carbohydrate metabolism instead of fat metabolism regulated by gut microbes mediates high-fat diet-induced obesity[J].Beneficial Microbes,2014,5(3):335-344.
[25] WANG Z,KLIPFELL E,BENNETT B J,et al.Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease[J].Nature,2011,472(7341):57-63.
[26] HOOPER L V.Do symbiotic bacteria subvert host immunity?[J].Nature Reviews Microbiology,2009,7(5):367-374.
[2] BENGMARK S.Gut microbiota,immune development and function[J].Pharmacological Research,2013,69(1):87-113.
[3] YILDIRIM S,YEOMAN C J,SIPOS M,et al.Characterization of the fecal microbiome from non-human wild primates reveals species specific microbial communities[J].PLoS One,2010,5(11):e13963.
[4] 赵娜,刘社兰,路纪琪,等.中国恒河猴肠道菌群特征揭示[J].生物技术通报,2013,29(7):153-160.
[5] 姚丽娟.不同年龄段神农架金丝猴肠道菌群组成和差异的研究[D].武汉:华中农业大学,2015.
[6] 王剑.健康和腹泻成年川金丝猴粪样菌群比较分析[D].雅安:四川农业大学,2015.
[7] GRIFFIN N W,AHERN P P,CHENG J Y,et al.Prior dietary practices and connections to a human gut microbial metacommunity alter responses to diet interventions[J].Cell Host & Microbe,2017,21(1):84-96.
[8] UENISHI G,FUJITA S,OHASHI G,et al.Molecular analyses of the intestinal microbiota of chimpanzees in the wild and in captivity[J].American Journal of Primatology,2007,69(4):367-376.
[9] BIAGI E,NYLUND L,CANDELA M,et al.Through ageing,and beyond:gut microbiota and inflammatory status in seniors and centenarians[J].PLoS One,2010,5(5):e10667.
[10] COSTELLO E K,GORDON J I,SECOR S M,et al.Postprandial remodeling of the gut microbiota in Burmese pythons[J].The ISME Journal,2010,4(11):1375-1385.
[11] ISMAIL N A,RAGAB S H,ELBAKY A A,et al.Frequency of firmicutes and bacteroidetes in gut microbiota in obese and normal weight Egyptian children and adults[J].Archives of Medical Science,2011,7(3):501-507.
[12] 简平,王强,王剑,等.不同年龄段川金丝猴肠道菌群结构差异分析[J].动物营养学报,2015,27(4):1302-1309.
[13] JEWELL K A,SCOTT J J,ADAMS S M,et al.A phylogenetic analysis of the phylum Fibrobacteres[J].Systematic and Applied Microbiology,2013,36(6):376-382.
[14] ZHOU X M,WANG B S,PAN Q,et al.Whole-genome sequencing of the snub-nosed monkey provides insights into folivory and evolutionary history[J].Nature Genetics,2014,46(12):1303-1310.
[15] WANG Y H,HUANG Y.Effect of Lactobacillus acidophilus and Bifidobacterium bifidum supplementation to standard triple therapy on Helicobacter pylori eradication and dynamic changes in intestinal flora[J].World Journal of Microbiology and Biotechnology,2014,30(3):847-853.
[16] TROTT D J,MCLAREN A J,HAMPSON D J.Pathogenicity of human and porcine intestinal spirochetes in one-day-old specific-pathogen-free chicks:an animal model of intestinal spirochetosis[J].Infection and Immunity,1995,63(9):3705-3710.
[17] ARUMUGAM M,RAES J,PELLETIER E,et al.Enterotypes of the human gut microbiome[J].Nature,2011,473(7346):174-180.
[18] SHINKAI T,UEKI T,KOBAYASHI Y.Detection and identification of rumen bacteria constituting a fibrolytic consortium dominated by Fibrobacter succinogenes[J].Animal Science Journal,2010,81(1):72-79.
[19] BIAN G R,MA L,SU Y,et al.The microbial community in the feces of the white rhinoceros(Ceratotherium simum)as determined by barcoded pyrosequencing analysis[J].PLoS One,2013,8(7):e70103.
[20] DALY K,PROUDMAN C J,DUNCAN S H,et al.Alterations in microbiota and fermentation products in equine large intestine in response to dietary variation and intestinal disease[J].British Journal of Nutrition,2012,107(7):989-995.
[21] CARLIER J P,BEDORA-FAURE M,K'OUAS G,et al.Proposal to unify Clostridium orbiscindens Winter et al.1991 and Eubacterium plautii(Séguin 1928)Hofstad and Aasjord 1982,with description of Flavonifractor plautii gen.nov.,comb.nov.,and reassignment of Bacteroides capillosus to Pseudoflavonifractor capillosus gen.nov.,comb.nov.[J].International Journal of Systematic and Evolutionary Microbiology,2010,60(3):585-590.
[22] MASLOWSKI K M,MACKAY C R.Diet,gut microbiota and immune responses[J].Nature Immunology,2011,12(1):5-9.
[23] EDITOR T.Microbes in your gut could be cause of allergies[J].Emerging Infectious Diseases.
[24] LI M,GU D,XU N,et al.Gut carbohydrate metabolism instead of fat metabolism regulated by gut microbes mediates high-fat diet-induced obesity[J].Beneficial Microbes,2014,5(3):335-344.
[25] WANG Z,KLIPFELL E,BENNETT B J,et al.Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease[J].Nature,2011,472(7341):57-63.
[26] HOOPER L V.Do symbiotic bacteria subvert host immunity?[J].Nature Reviews Microbiology,2009,7(5):367-374.