The present study was designed to reveal the rumen bacterial diversity in Jinjiang cattle using MiSeq high-flux sequencing technology. Ruminal liquid samples were obtained from three Jinjiang cattles (bull) weighted (400±20) kg with permanent rumen cannulas. Total DNA was extracted and the 16S rDNA V4 to V5 of bacteria was sequenced by MiSeq sequencing technology. The abundance, distribution and α-diversity index of species were analyzed. The results showed that a total of 56 763 valid 16S rDNA sequences and 946 operational taxonomic unit (OTU) across 3 samples were obtained. The richness indexes, Chao and Ace indexes, of ruminal bacterial were 836 and 841, respectively; and alpha diversity indexes, Shannon and Simpson indexes were 4.96 and 0.021 5, respectively. Fifteen phyla, 23 classes, 26 families and 44 genera were identified via taxonomic summary. The dominant phyla among them were Bacteroidetes (64.37%), Firmicutes (21.20%) and Proteobacteria (7.59%). The most abundant classes were Bacteroidia (52.88%), Clostridia (17.03%), and Prevotellaceae (36.26%). Ruminococcaceae (9.33%) and Lachnospiraceae (4.89%) were the predominant family. At genus level, the high abundance of genera were Prevotella (28.97%), Paraprevotella (3.08%), Rikenella (2.28%), Clostridium Ⅳ (1.77%), Succiniclastium (1.62%) and Ruminococcus (1.53%). In conclusion, the diversity of rumen bacterial community in Jinjiang cattle is low. Bacteroidetes is the predominant phylum and Firmicutes is the second most abundant phylum. Prevolla is the most abundant genus in the rumen bacterial community.
GAO Yufei
,
OUYANG Kehui
,
QU Mingren
,
XIONG Xiaowen
,
WEN Qingqi
,
XU Lanjiao
. Analysis of Rumen Bacterial Diversity in Jinjiang Cattle Using MiSeq Sequencing Technology[J]. Chinese Journal of Animal Nutrition, 2016
, 28(1)
: 244
-248
.
DOI: 10.3969/j.issn.1006-267x.2016.01.031
[1] BÄCKHED F,LEY R E,SONNENBURG J L,et al.Host-bacterial mutualism in the human intestine[J].Science,2005,307(5717):1915-1920.
[2] 刘开朗,卜登攀,王加启,等.六个不同品种牛的瘤胃微生物群落的比较分析[J].中国农业大学学报,2009,14(1):13-18.
[3] ECKBURG P B,BIK E M,BERNSTEIN C N,et al.Diversity of the human intestinal microbial flora[J].Science,2005,308(5728):1635-1638.
[4] 石鹏君,柏映国,袁铁铮,等.应用rpoB和16S rDNA基因的变性梯度凝胶电泳技术对山羊瘤胃细菌多样性的研究[J].微生物学报,2007,47(2):285-289.
[5] DE LA FUENTE G,BELANCHE A,ABECIA L,et al.Rumen protozoal diversity in the Spanish ibex (Capra pyrenaica hispanica) as compared with domestic goats (Capra hircus)[J].European Journal of Protistology,2009,45(2):112-120.
[6] SHI P J,MENG K,ZHOU Z G,et al.The host species affects the microbial community in the goat rumen[J].Letters in Applied Microbiology,2008,46(1):132-135.
[7] JAMI E,MIZRAHI I.Composition and similarity of bovine rumen microbiota across individual animals[J].PLoS One,2012,7(3):e33306.
[8] ASMA Z,SYLVIE C,LAURENT C,et al.Microbial ecology of the rumen evaluated by 454 GS FLX pyrosequencing is affected by starch and oil supplementation of diets[J].FEMS Microbiology Ecology,2013,83(2):504-514.
[9] GUO W,LI Y,WANG L Z,et al.Evaluation of composition and individual variability of rumen microbiota in yaks by 16S rRNA high-throughput sequencing technology[J].Anaerobe,2015,34:74-79.
[10] PITTA D W,PINCHAK W E,DOWD S E,et al.Rumen bacterial diversity dynamics associated with changing from Bermudagrass hay to grazed winter wheat diets[J].Microbial Ecology,2010,59(3):511-522.
[11] 裴彩霞,毛胜勇,朱伟云.山羊瘤胃产甲烷古菌多样性及与其他动物瘤胃的比较[J].畜牧兽医学报,2012,43(6):909-914.
[12] KOBYASHI Y.Inclusion of novel bacteria in rumen microbiology:need for basic and applied science[J].Animal Science Journal,2006,77(4):375-385.
[13] LENG J,CHENG Y M,ZHANG C Y,et al.Molecular diversity of bacteria in Yunnan yellow cattle (Bos taurs) from Nujiang region,China[J].Molecular Biology Reports,2012,39(2):1181-1192.
[14] PETRI R M,SCHWAIGER T,PENNER G B,et al.Characterization of the core rumen microbiome in cattle during transition from forage to concentrate as well as during and after an acidotic challenge[J].PLoS One,2013,8(12):e83424.
[15] PINLOCHE E,MCEWAN N,MARDEN J P,et al.The effects of a probiotic yeast on the bacterial diversity and population structure in the rumen of cattle[J].PLoS One,2013,8(7):e67824.
[16] LI R W,WU S,BALDWIN R T,et al.Perturbation dynamics of the rumen microbiota in response to exogenous butyrate[J].PLoS One,2012,7(1):e29392.
[17] 李亚丹.芒草驯养湘西黄牛(Bos taurus)瘤胃微生物多样性及β-葡萄糖苷酶新基因的克隆与表达研究[D].博士学位论文.长沙:湖南农业大学,2012.
[18] 杜占池,杜菁昀.我国不同自然区域天然牧地和人工牧地营养价值的比较研究[J].中国草地,2003,5(1):232-276.
[19] RAMAK A,PETERKA M,TAJIMA K,et al.Unravelling the genetic diversity of ruminal bacteria belonging to the CFB phylum[J].FEMS Microbiology Ecology,2000,33(1):69-79.
[20] BEKELE A Z,KOIKE S,KOBAYASHI Y.Genetic diversity and diet specificity of ruminal Prevotella arevealed by 16S rRNA gene-based analysis[J].FEMS Microbiology Letters,2010,305(1):49-57.
[21] GARDNER R G,WELLS J E,RUSSELL J B,et al.The cellular location of Prevotella ruminicola beta-1,4-D-endoglucanase and its occurrence in other strains of ruminal bacteria[J].Applied and Environmental Microbiology,1995,61(9):3288-3292.
[22] KRAUSE D O,DENMAN S E,MACKIE R I,et al.Opportunities to improve fiber degradation in the rumen:microbiology,ecology,and genomics[J].FEMS Microbiology Reviews,2003,27(5):663-693.
[23] GRUNINGER R J,SENSEN C W,MCALLISTER T A,et al.Diversity of rumen bacteria in Canadian cervids[J].PLoS One,2014,9(2):e89682.
[24] 刘晶.饲料果胶对瘤胃微生物菌群结构和微生物蛋白合成影响的研究[D].博士学位论文.杭州:浙江大学,2014.
[25] HUO W J,ZHU W Y,MAO S Y.Impact of subacute ruminal acidosis on the diversity of liquid and solid-associated bacteria in the rumen of goats[J].World Journal of Microbiology and Biotechnology,2014,30(2):669-680.
