研究简报 Short communications

不同粗饲料条件下梅花鹿瘤胃甲烷菌结构的比较分析

  • 李志鹏 ,
  • 刘晗璐 ,
  • 司华哲 ,
  • 鲍坤 ,
  • 李光玉
展开
  • 中国农业科学院特产研究所经济动物研究室, 长春 130112

收稿日期: 2016-03-03

  网络出版日期: 2016-09-08

基金资助

国家自然科学基金(31501984);吉林省重大科技攻关专项(20140203018NY)

Comparative Analysis of Methanogen Community in Rumen of Sika Deer (Cervus nippon) under Different Forages

  • LI Zhipeng ,
  • LIU Hanlu ,
  • SI Huazhe ,
  • BAO Kun ,
  • LI Guangyu
Expand
  • Department of Speical Animal Nutrition and Feed, Insitute of Special Animal and Plant Sciences of Chinese Academy of Agricultural Sciences, Changchun 130112, China

Received date: 2016-03-03

  Online published: 2016-09-08

摘要

本研究旨在基于高通量测序技术分析比较采食3种常见粗饲料梅花鹿瘤胃甲烷菌结构。选取3只2岁龄的装有永久性瘤胃瘘管的成年雄性梅花鹿为研究对象,采用3×3拉丁方设计,分别饲喂以柞树叶(OL组)、玉米秸秆(CS组)和玉米青贮(CI组)为主要粗饲料的饲粮。预试期为1周,正试期为4周。采用引物A519F、A976R扩增瘤胃甲烷菌16S rRNA基因V3~V4区,基于Illumina Miseq PE250平台进行测序。结果表明:9个样本共获得600 352条高质量的甲烷菌16S rRNA基因序列,基于97%相似性共归为111个分类操作单元(OTU)。覆盖度指数表明本试验样品覆盖了瘤胃99%的甲烷菌。分类分析结果表明甲烷短杆菌属(Methanobrevibacter spp.)[OL组:(97.80±6.00)%;CS组:(97.10±1.50)%;CI组:(87.50±5.50)%]是梅花鹿瘤胃优势甲烷菌,但采食3种粗饲料梅花鹿瘤胃甲烷菌在种水平的分布有差异。CI组Methanosphaera stadtmanae相对丰度显著高于OL组与CS组(P<0.05)。OL组与CI组Methanobrevibacter millerae相对丰度高于CS组(P>0.05),OL组与CS组Methanobrevibacter boviskoreani相对丰度高于CI组(P>0.05),而CS组与CI组Methanobrevibacter olleyae相对丰度高于OL组(P>0.05)。本研究发现Methanobrevibacter spp.是梅花鹿瘤胃优势甲烷菌。

本文引用格式

李志鹏 , 刘晗璐 , 司华哲 , 鲍坤 , 李光玉 . 不同粗饲料条件下梅花鹿瘤胃甲烷菌结构的比较分析[J]. 动物营养学报, 2016 , 28(9) : 2911 -2919 . DOI: 10.3969/j.issn.1006-267x.2016.09.030

Abstract

The objective of present study was to compare the methanogen community in the rumen of sika deer (Cervus nippon) fed three common forages using the high throughput sequencing technology. Three 2-year-old male adult Sika deers with permanent ruminal cannulas were used as experimental animal in a 3×3 Latin square design, and their fed diets with oak with leaf (OL group), corn stover (CS group) and corn silage (CI group) as main forage, respectively. After one week of adaption to the diets, sika deer received each diet for 4 weeks. The primers A519F and A976R were used to amplify the V3 to V4 regions of the methanogen 16S rRNA gene. The amplicon was then sequenced on the Illumina MiSeq PE250 platform. The results showed as follows: a total of 600 352 high quality methanogen 16S rRNA gene sequences were obtained from 9 samples. These sequences were classified into 111 operational taxonomic units (OTU) based on 97% sequence similarity. Coverage index showed that 99% of the methanogen species were represented in any given rumen sample. The results of taxonomic analysis showed that Methanobrevibacter spp. [OL group: (97.80±6.00)%; CS group: (97.10±1.50)%; CI group: (87.50±5.50)%] was the dominant methanogen in the rumen of sika deer. However, the distribution of methanogen at species level was different among the three groups. The relative abundance of Methanosphaera stadtmanae in the CI group was significantly higher than that in the OL and CS groups (P<0.05). The relative abundance of Methanobrevibacter millerae was increased in the OL and CI groups compared with the CS group (P>0.05). The relative abundance of Methanobrevibacter boviskoreani in the OL and CS groups was higher than that in the CI group (P>0.05). While, the relative abundance of Methanobrevibacter olleyae in the CS and CI groups was increased compared with the OL group (P>0.05). These results suggest that Methanobrevibacter spp. is the dominant methanogen in rumen of sika deer.

参考文献

[1] GILL M,SMITH P,WILKINSON J M.Mitigating climate change:the role of domestic livestock[J].Animal,2010,4(3):323-333.  
[2] JOHNSON K A,JOHNSON D E.Methane emissions from cattle[J].Journal of Animal Science,1995,73(8):2483-2492.  
[3] JANSSEN P H,KIRS M.Structure of the archaeal community of the rumen[J].Applied and Environmental Microbiology,2008,74(12):3619-3625.  
[4] ST-PIERRE B,WRIGHT A D G.Diversity of gut methanogens in herbivorous animals[J].Animal,2013,7(Suppl.1):49-56.
[5] LI Z P,WRIGHT A D G,LIU H L,et al.Bacterial community composition and fermentation patterns in the rumen of sika deer (Cervus nippon) fed three different diets[J].Microbial Ecology,2015,69(2):307-318.  
[6] TAN H Y,SIEO C C,ABDULLAH N,et al.Effects of condensed tannins from Leucaena on methane production,rumen fermentation and populations of methanogens and protozoa in vitro[J].Animal Feed Science and Technology,2011,169(3/4):185-193.
[7] LI Z P,ZHANG Z G,XU C,et al.Bacteria and methanogens differ along the gastrointestinal tract of Chinese roe deer (Capreolus pygargus)[J].PLoS One,2014,9(12):e114513.
[8] CAPORASO J G,KUCZYNSKI J,STOMBAUGH J,et al.QIIME allows analysis of high-throughput community sequencing data[J].Nature Methods,2010,7(5):335-336.  
[9] EDGAR R C.Search and clustering orders of magnitude faster than BLAST[J].Bioinformatics,2010,26(19):2460-2461.  
[10] DESANTIS T Z,HUGENHOLTZ P,LARSEN N,et al.Greengenes,a chimera-checked 16S rRNA gene database and workbench compatible with ARB[J].Applied and Environmental Microbiology,2006,72(7):5069-5072.  
[11] HAAS B J,GEVERS D,EARL A M,et al.Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons[J].Genome Research,2011,21(3):494-504.  
[12] TAMURA K,PETERSON D,PETERSON N,et al.MEGA5:molecular evolutionary genetics analysis using maximum likelihood,evolutionary distance,and maximum parsimony methods[J].Molecular Biology and Evolution,2011,28(10):2731-2739.  
[13] HUNGATE R E.Hydrogen as an intermediate in the rumen fermentation[J].Archiv für Mikrobiologie,1967,59(1/2/3):158-164.
[14] WRIGHT A D G,MA X L,OBISPO N E.Methanobrevibacter phylotypes are the dominant methanogens in sheep from Venezuela[J].Microbial Ecology,2008,56(2):390-394.  
[15] CERSOSIMO L M,LACHANCE H,ST-PIERRE B,et al.Examination of the rumen bacteria and methanogenic archaea of wild impalas (Aepyceros melampus melampus) from Pongola,South Africa[J].Microbial Ecology,2015,69(3):577-585.  
[16] HOOK S E,STEELE M A,NORTHWOOD K S,et al.Impact of high-concentrate feeding and low ruminal pH on methanogens and protozoa in the rumen of dairy cows[J].Microbial Ecology,2011,62(1):94-105.  
[17] KONG Y H,XIA Y,SEVIOUR R,et al.Biodiversity and composition of methanogenic populations in the rumen of cows fed alfalfa hay or triticale straw[J].FEMS Microbiology Ecology,2013,84(2):302-315.  
[18] 杨承剑,韦升菊,梁辛,等.利用16S rRNA基因克隆文库技术分析德昌水牛瘤胃产甲烷菌的多样性[J].湖南农业大学学报:自然科学版,2014,40(4):382-388.
[19] SUNDSET M A,EDWARDS J E,CHENG Y F,et al.Rumen microbial diversity in svalbard reindeer,with particular emphasis on methanogenic archaea[J].FEMS Microbiology Ecology,2009,70(3):553-562.  
[20] CHAUDHARY P P,SIROHI S K,SAXENA J.Diversity analysis of methanogens in rumen of Bubalus bubalis by 16S riboprinting and sequence analysis[J].Gene,2012,493(1):13-17.  
[21] HUANG X D,TAN H Y,LONG R J,et al.Comparison of methanogen diversity of yak (Bos grunniens) and cattle (Bos taurus) from the Qinghai-Tibetan plateau,China[J].BMC Microbiology,2012,12(1):237.
[22] ZHOU M,HERNANDEZ-SANABRIA E,GUAN L L.Characterization of variation in rumen methanogenic communities under different dietary and host feed efficiency conditions,as determined by PCR-denaturing gradient gel electrophoresis analysis[J].Applied and Environmental Microbiology,2010,76(12):3776-3786.  
[23] KITTELMANN S,PINARES-PATIÑO C S,SEEDORF H,et al.Two different bacterial community types are linked with the low-methane emission trait in sheep[J].PLoS One,2014,9(7):e103171.
[24] GOOPY J P,DONALDSON A,HEGARTY R,et al.Low-methane yield sheep have smaller rumens and shorter rumen retention time[J].British Journal of Nutrition,2014,111(4):578-585.  
[25] REA S,BOWMAN J P,POPOVSKI S,et al.Methanobrevibacter millerae sp.nov.and Methanobrevibacter olleyae sp.nov.,methanogens from the ovine and bovine rumen that can utilize formate for growth[J].International Journal of Systematic and Evolutionary Microbiology,2007,57(3):450-456.  
[26] PURUSHE J,FOUTS D E,MORRISON M,et al.Comparative genome analysis of Prevotella ruminicola and Prevotella bryantii:insights into their environmental niche[J].Microbial Ecology,2010,60(4):721-729.  
[27] BORREL G,HARRIS H M B,TOTTEY W,et al.Genome sequence of "Candidatus Methanomethylophilus alvus" Mx1201,a methanogenic archaeon from the human gut belonging to a seventh order of methanogens[J].Journal of Bacteriology,2012,194(24):6944-6945.  
[28] POULSEN M,SCHWAB C,JENSEN B B,et al.Methylotrophic methanogenic Thermoplasmata implicated in reduced methane emissions from bovine rumen[J].Nature Communications,2013,4:1428.
[29] MCSWEENEY C S,PALMER B,MCNEILL D M,et al.Microbial interactions with tannins:nutritional consequences for ruminants[J].Animal Feed Science and Technology,2001,91(1/2):83-93.
[30] FRICKE W F,SEEDORF H,HENNE A,et al.The genome sequence of Methanosphaera stadtmanae reveals why this human intestinal archaeon is restricted to methanol and H2 for methane formation and ATP synthesis[J].Journal of Bacteriology,2006,188(2):642-658.  
[31] CARLOLINE CHAE-HYUN K.Identification of rumen methanogens,characterization of substrate requirements and measurement of hydrogen thresholds[D].MSc.Thesis.Palmerston North:Massey University,2012.
[32] LEE J H,KUMAR S,LEE G H,et al.Methanobrevibacter boviskoreani sp.nov.,isolated from the rumen of Korean native cattle[J].International Journal of Systematic and Evolutionary Microbiology,2013,63(11):4196-4201.
[33] 陶莲,刁其玉.青贮发酵对玉米秸秆品质及菌群构成的影响[J].动物营养学报,2016,28(1):198-207.
文章导航

/