健康中国荷斯坦奶牛不同发育阶段瘤胃的菌群多样性研究
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摘要
为了分析不同发育阶段健康中国荷斯坦奶牛瘤胃菌群结构多样性,试验采用16S r DNA高通量测序技术对抽提的4个阶段健康奶牛瘤胃内容物的细菌基因组总DNA进行OTUs聚类、超1(Chao1)指数、香浓(Shannon)指数及OTUs交叠分析。结果表明:哺乳犊牛瘤胃中主要以普氏菌属-7(46.0%)、毛罗菌科NK3A20(8.9%)、罗氏菌属(4.9%)为主;断奶犊牛瘤胃中主要以普氏菌属-7(31.0%)、毛罗菌科NK3A20(16.0%)、理研菌科RC9-gut-group(2.3%)为主;青成牛瘤胃内的普氏菌属-1(8.5%)、丹毒丝菌科UCG-004(7.5%)、反刍杆菌属(6.4%)、琥珀酸弧菌科UCG-002(5.4%)、普氏菌科UCG-003(4.9%)、理研菌科RC9-gut-group(4.6%)的相对丰度较高;成年牛瘤胃内的普氏菌属-1(38.0%)、琥珀酸弧菌科UCG-0019(4.5%)、理研菌科RC9-gut-group(2.3%)、普氏菌科UCG-003(2.2%)、琥珀酸弧菌科UCG-002(2.1%)、普氏菌属-7(1.5%)相对丰度较高。说明4个阶段中国荷斯坦奶牛瘤胃菌群结构存在明显差异,其中哺乳犊牛与断奶犊牛瘤胃菌群属丰度低、结构简单,青成牛与成年牛瘤胃菌群丰度高、结构复杂。
The aim of the present study was to explore the rumen microflora structure characteristics at different development stages of healthy China Holstein cows.The total DNA of bacteria from four stages of healthy dairy cattle rumen contents were extracted and sequenced by using 16S rDNA high-throughput sequencing technique.Then the sequences were subjected to OTUs cluster analysis,Chao 1 and Shannon Index analysis and OTUs overlap analysis.The results showed that the main bacteria were Prevotella-7(46.0%),Lachnospiraceae NK3 A20(8.9%)and Roseburia(4.9%) in the rumen of suckling calves.The main bacteria were Prevotella-7(31.0%),Lachnospiraceae NK3 A20(16.0%)and Rikenellaceae-RC9-gut-group(2.3%) in the rumen of weaning calf.The relative abundance of Prevotella-1(8.5%) 、Erysipelotrichaceae UCG-004(7.5%),Ruminobacter(6.4%),Succinivibrionaceae UCG-002(5.4%),Prevotellaceae UCG-003(4.9%) and Rikenellaceae-RC9-gut-group(4.6%) was higher in the heifer rumen.The relative abundance of Prevotella-1(38.0%),Succinivibrionaceae UCG-0019(4.5%),Rikenellaceae-RC9-gut-group(2.3%),Prevotellaceae UCG-003(2.2%),Succinivibrionaceae UCG-002(2.1%),Prevotella-7(1.5%) was higher in the rumen of adult cattle.The results indicated that there were significant differences in rumen microflora between China Holstein cows at the four stages.The flora of rumen bacteria in sucking and weaning calf was low in abundance and simple in structure.The abundance of rumen bacteria in heifer and adult cows was high and the structure was complex.
The aim of the present study was to explore the rumen microflora structure characteristics at different development stages of healthy China Holstein cows.The total DNA of bacteria from four stages of healthy dairy cattle rumen contents were extracted and sequenced by using 16S rDNA high-throughput sequencing technique.Then the sequences were subjected to OTUs cluster analysis,Chao 1 and Shannon Index analysis and OTUs overlap analysis.The results showed that the main bacteria were Prevotella-7(46.0%),Lachnospiraceae NK3 A20(8.9%)and Roseburia(4.9%) in the rumen of suckling calves.The main bacteria were Prevotella-7(31.0%),Lachnospiraceae NK3 A20(16.0%)and Rikenellaceae-RC9-gut-group(2.3%) in the rumen of weaning calf.The relative abundance of Prevotella-1(8.5%) 、Erysipelotrichaceae UCG-004(7.5%),Ruminobacter(6.4%),Succinivibrionaceae UCG-002(5.4%),Prevotellaceae UCG-003(4.9%) and Rikenellaceae-RC9-gut-group(4.6%) was higher in the heifer rumen.The relative abundance of Prevotella-1(38.0%),Succinivibrionaceae UCG-0019(4.5%),Rikenellaceae-RC9-gut-group(2.3%),Prevotellaceae UCG-003(2.2%),Succinivibrionaceae UCG-002(2.1%),Prevotella-7(1.5%) was higher in the rumen of adult cattle.The results indicated that there were significant differences in rumen microflora between China Holstein cows at the four stages.The flora of rumen bacteria in sucking and weaning calf was low in abundance and simple in structure.The abundance of rumen bacteria in heifer and adult cows was high and the structure was complex.
引文
[1]张成岗.当前慢病防控困境迫切呼唤新医学和菌心说[J].科技导报,2015,33(22):106-111.
[2]ADG W,KLIEVE A V.Does the complexity of the rumen microbial ecology preclude methane mitigation[J].Anim Feed Sci Technol,2011,167(7):248-253.
[3]田彦.基于高通量测序的中国荷斯坦奶牛瘤胃宏转录组研究[D].北京:中国科学院大学,2015.
[4]KELLENBERGER E.Exploring the unknown:The silent revolution of microbiology[J].EMBO Rep,2001,2(1):5-7.
[5]JORDAND D B,WAGSCHAL K.Properties and applications of microbial beta-D-xylosidases featuring the catalytically efficient enzyme from Selenomonas ruminantium[J].Appl Microbiol Biotechnol,2010,86(6):1647-1658.
[6]TORSVIK V,OVREAS L.Microbial diversity and function in soil:from genes to ecosystems[J].Curr Opin Microbiol,2002,5(3):240.
[7]王星凌,赵红波,游伟,等.不同蛋白质和碳水化合物饲料来源对牛瘤胃蛋白质代谢的定量研究[J].广西农学报,2010,25(5):37-39.
[8]WANG Q,GARRITY G M,TIEDJE J M,et al.Naive bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy[J].Appl Environ Microbiol,2007,73(16):5261.
[9]QUAST C,PRUESSE E,YILMAZ P,et al.The SILVA ribosomal RNA gene database project:improved data processing and webbased tools[J].Nucleic Acids Res,2013,41:D590-596.
[10]高权新,吴天星,王进波.肠道微生物与寄主的共生关系研究进展[J].动物营养学报,2010,22(3):519-526.
[11]HARASZTHY V I,ZAMBON J J,SREENIVASAN P K,et al.Identification of oral bacterial species associated with halitosis[J].J Am Dent Asso,2007,138(8):1113-1120.
[12]BAR-PELED U,ROBINZON B,MALTZ E,et al.Increased weightgain and effects on production parameters of holstein heifercalves that were allowed to suckle from birth to six weeksof age[J].J Dairy Sci,1997,80:2523-2528.
[13]LI M,PENNER G B,HERNANDEZSANABRIA E,et al.Effects of sampling location and time,and host animal on assessment of bacterial diversity and fermentation parameters in the bovine rumen[J].J Appl Microbiol,2009,107(6):1924-1934.
[14]李伟,韩云胜,袁雪,等.断奶犊牛瘤胃细菌16S r DNA文库的构建及多样性分析[J].黑龙江畜牧兽医,2015(12上):83-87.
[15]KIM M,MORRISON M,YU Z.Status of the phylogenetic diversity census of ruminal microbiomes[J].Fems Microbiol Ecol,2011,76(1):49-63.
[16]STEVENSON D M,WEIMER P J.Dominance of Prevotella and low abundance of classical ruminal bacterial species in the bovine rumen revealed by relative quantification real-time PCR[J].Appl Microbiol Biotechnol,2007,75(1):165-174.
[17]MICHELLAND R J,MONTEILS V,ZENED A,et al.Spatial and temporal variations of the bacterial community in the bovine digestive tract[J].J Appl Microbiol,2009,107(5):1642-1650.
[18]WONGWILAIWALIN S,LAOTHANACHAREON T,MHUANTONG W,et al.Comparative metagenomic analysis of microcosm structures and lignocellulolytic enzyme systems of symbiotic biomass-degrading consortia[J].Appl Microbiol Biotechnol,2013,97(20):8941-8954.
[2]ADG W,KLIEVE A V.Does the complexity of the rumen microbial ecology preclude methane mitigation[J].Anim Feed Sci Technol,2011,167(7):248-253.
[3]田彦.基于高通量测序的中国荷斯坦奶牛瘤胃宏转录组研究[D].北京:中国科学院大学,2015.
[4]KELLENBERGER E.Exploring the unknown:The silent revolution of microbiology[J].EMBO Rep,2001,2(1):5-7.
[5]JORDAND D B,WAGSCHAL K.Properties and applications of microbial beta-D-xylosidases featuring the catalytically efficient enzyme from Selenomonas ruminantium[J].Appl Microbiol Biotechnol,2010,86(6):1647-1658.
[6]TORSVIK V,OVREAS L.Microbial diversity and function in soil:from genes to ecosystems[J].Curr Opin Microbiol,2002,5(3):240.
[7]王星凌,赵红波,游伟,等.不同蛋白质和碳水化合物饲料来源对牛瘤胃蛋白质代谢的定量研究[J].广西农学报,2010,25(5):37-39.
[8]WANG Q,GARRITY G M,TIEDJE J M,et al.Naive bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy[J].Appl Environ Microbiol,2007,73(16):5261.
[9]QUAST C,PRUESSE E,YILMAZ P,et al.The SILVA ribosomal RNA gene database project:improved data processing and webbased tools[J].Nucleic Acids Res,2013,41:D590-596.
[10]高权新,吴天星,王进波.肠道微生物与寄主的共生关系研究进展[J].动物营养学报,2010,22(3):519-526.
[11]HARASZTHY V I,ZAMBON J J,SREENIVASAN P K,et al.Identification of oral bacterial species associated with halitosis[J].J Am Dent Asso,2007,138(8):1113-1120.
[12]BAR-PELED U,ROBINZON B,MALTZ E,et al.Increased weightgain and effects on production parameters of holstein heifercalves that were allowed to suckle from birth to six weeksof age[J].J Dairy Sci,1997,80:2523-2528.
[13]LI M,PENNER G B,HERNANDEZSANABRIA E,et al.Effects of sampling location and time,and host animal on assessment of bacterial diversity and fermentation parameters in the bovine rumen[J].J Appl Microbiol,2009,107(6):1924-1934.
[14]李伟,韩云胜,袁雪,等.断奶犊牛瘤胃细菌16S r DNA文库的构建及多样性分析[J].黑龙江畜牧兽医,2015(12上):83-87.
[15]KIM M,MORRISON M,YU Z.Status of the phylogenetic diversity census of ruminal microbiomes[J].Fems Microbiol Ecol,2011,76(1):49-63.
[16]STEVENSON D M,WEIMER P J.Dominance of Prevotella and low abundance of classical ruminal bacterial species in the bovine rumen revealed by relative quantification real-time PCR[J].Appl Microbiol Biotechnol,2007,75(1):165-174.
[17]MICHELLAND R J,MONTEILS V,ZENED A,et al.Spatial and temporal variations of the bacterial community in the bovine digestive tract[J].J Appl Microbiol,2009,107(5):1642-1650.
[18]WONGWILAIWALIN S,LAOTHANACHAREON T,MHUANTONG W,et al.Comparative metagenomic analysis of microcosm structures and lignocellulolytic enzyme systems of symbiotic biomass-degrading consortia[J].Appl Microbiol Biotechnol,2013,97(20):8941-8954.