云南大额牛瘤胃微生物多样性分析

doi:10.16431/j.cnki.1671-7236.2016.05.006

›› 2016, Vol. 43 ›› Issue (5): 1162-1168.doi: 10.16431/j.cnki.1671-7236.2016.05.006

云南大额牛瘤胃微生物多样性分析

周熊艳, 王松明, 顾招兵, 吴锡川, 冷静, 毛华明, 李清, 冯励, 杨舒黎

云南农业大学动物营养与饲料科学重点实验室, 昆明 650201

收稿日期:2016-01-06 出版日期:2016-05-20 发布日期:2016-05-23
通讯作者: 杨舒黎 E-mail:yangshuli77@163.com
作者简介:周熊艳(1991-),女,湖北荆州人,硕士生,研究方向:反刍动物营养与微生物工程,E-mail:1013233751@qq.com
基金资助:
国家自然科学基金(31160467、31360562、31160449、31260543)

Diversity Analysis of Rumen Microbes in Yunnan Gayals (Bos frontalis)

ZHOU Xiong-yan, WANG Song-ming, GU Zhao-bing, WU Xi-chuan, LENG Jing, MAO Hua-ming, LI Qing, FENG Li, YANG Shu-li

Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming 650201, China

Received:2016-01-06 Online:2016-05-20 Published:2016-05-23

摘要/Abstract

摘要： 为研究云南大额牛瘤胃微生物多样性,本研究通过对大额牛瘤胃微生物宏基因组测序(总数据产出>3Gb)、分析、组装,共获得13546196个环境基因标签(EGTs)。在微生物分析时随机选用了10387566个EGTs(占总EGTs的76.68%)与NCBI的NR数据库进行BLAST比对,进行物种注释。结果显示,在分析的EGTs中,主要由细菌域、真核生物域、古生菌域及部分不能确定域归属的未知微生物构成,其中微生物主要属于10个门,94%的EGTs属于拟杆菌门、厚壁菌门、变形杆菌门和放线菌门,拟杆菌门和厚壁菌门丰度最高,分别占总细菌的48%和42%。大额牛瘤胃中主要的纤维降解细菌为黄化瘤胃球菌、溶纤维丁酸弧菌、白色瘤胃球菌和产琥珀酸丝状杆菌,分别占总细菌的1.60%、1.20%、0.86%和0.52%。本研究结果表明EGTs技术可用于分析环境微生物群落结构和解释微生物群落功能,对研究特殊环境中的微生物的构成具有重要意义。

关键词: 云南大额牛; 宏基因组测序; 环境基因标签; 微生物群落

Abstract: In order to study the rumen microbial diversity in Yunnan gayals (Bos frontalis), we analyzed the diversity of microbes using largely assembled sequence data obtained by metagenomic sequencing DNA isolated from rumen samples of eight adult galyals. The genome primary sequence (total metagenome size was >3 Gb) was assembled with short reads.Based on the gayal rumen microbial metagenomic sequencing, we received a total of 13 546 196 EGTs. Because of the relatively large amount, 10 387 566 EGTs (76.68% of all EGTs ) were randomly selected to analyze microbial communities by BLAST search of the NCBI-NR database. Microbial species annotations analysis revealed that microbial communities from gayals rumen were mainly composed of the bacterial domain, eukarya domain, archaea domain and unknown microbial composition. The majority microbes mainly belonged to ten phylums, and 94% EGTs belonged to Bacteroidetes, Firmicutes, Proteobacteria and Actinobacteria, of which the highest abundance phylums were Bacteroidete and Firmicutes, accounting for 48% and 42%, respectively. In addition, the main cellulolytic bacteria in rumen of gayals were Ruminococcus flavefacie, Butyrivibrio fibrisolvens, Ruminococcus albus and Fibrobacter succinogenes. They accounted for 1.60%, 1.20%, 0.86% and 0.52% of the total bacteria, respectively. These results further indicated that EGTs data could be used to analyze and explain environmental microbial community structure and function. There was great significance to study the composition of microorganisms in special environments.

Key words: Yunnan gayals (Bos frontalis); metagenomics sequences; EGTs; microbial communities

中图分类号:

S823

周熊艳, 王松明, 顾招兵, 吴锡川, 冷静, 毛华明, 李清, 冯励, 杨舒黎. 云南大额牛瘤胃微生物多样性分析[J]. , 2016, 43(5): 1162-1168.

ZHOU Xiong-yan, WANG Song-ming, GU Zhao-bing, WU Xi-chuan, LENG Jing, MAO Hua-ming, LI Qing, FENG Li, YANG Shu-li. Diversity Analysis of Rumen Microbes in Yunnan Gayals (Bos frontalis)[J]. , 2016, 43(5): 1162-1168.

参考文献

[1] Nalbantoglua U,Cakar A,Dogan H,et al.Metagenomic analysis of the microbial community in kefir grains[J].Food Microbiology,2014,41(6):42-51.
[2] Tomazetto G,Wibberg D,Schlüter A,et al.New FeFe-hydrogenase genes identified in a metagenomic fosmid library from a municipal wastewater treatment plant as revealed by high-throughput sequencing[J].Res Microbiol,2015,166(1):9-19.
[3] Alcaraz L D,Belda-Ferre P,Cabrera-Rubio R,et al.Identifying a healthy oral microbiome through metagenomics[J].Clin Microbiol Infect,2012,18(4):54-57.
[4] Eckburg P B,Bik E M,Bemstein C N,et al.Diversity of the human intestinal microbial flora[J].Science,2005,308(6):1635-1638.
[5] Tringe S G,von Mering C,Kobayashi A,et al.Comparative metagenomics of microbial communities[J]. Science,2005,308(3):554-557.
[6] 毛华明,邓卫东,文际坤.大额牛(Bos frontalis)的生物学特征及研究开发利用潜力[J].云南农业大学学报,2005,20(3):258-261.
[7] Huque K S,Rahman M M,Jalil M A.Nutritive value of major feeding redients,usually browsed and their responses to gayals (Bos frontalis)in the hill tractarea[J].Biol Sci,2001,4:1559-1561.
[8] Huque K S,Rahman M M,Jalil M A. Study on the growth pattern of gayal and their crossbred calves[J]. Anim Sci,2001,14(9):1245-1249.
[9] 王利平.不同日粮对大额牛瘤胃发酵和瘤胃微生物区系的影响[D].昆明:云南农业大学,2006.
[10] 李碧凤,朱雅新,苟潇,等.云南大额牛瘤胃宏基因组Fosmid文库的构建与分析[J].中国畜牧兽医,2013,40(12):61-65.
[11] Yang S L,Ma S C,Chen J,et al. Bacterial diversity in the rumen of Bos frontalis,Bubalus bubalis and Holstein cow as revealed by cloned 16S rRNA gene sequences[J]. Molecular Biology Reports,2010,37(4): 2063-2073.
[12] Leng J,Xie L J,Zhu R J,et al.Dominant bacterial communities in the rumen of gayals (Bos frontalis),yaks (Bos grunniens)and Yunnan Yellow cattle (Bos taurs) revealed by denaturing gradient gelelectrophoresis[J].Molecular Biology Reports,2010,38(8):4863-4872.
[13] Dehority B A.Rumen Microbiology[M].UK:Nottingham University Press,2003.
[14] 冯仰廉.反刍动物营养学[M].北京:科学出版社,2006.
[15] Ley R E,Turnbaugh P J,Klein S,et al.Microbial ecology:Human gut microbes associated with obesity[J].Nature,2006,444(12):1022-1023.
[16] Qin J,Li R,Raes J,et al. A human gut microbial gene catalogue established by metagenomics sequencing[J].Nature,2010,464(3):59-65.
[17] Tun H M, Brar M S, Khin N,et al.Dowd SE gene-centric metagenomics analysis of feline intestinal microbiome using 454 junior pyrosequencing[J].Microbiol Methods,2012,88(3): 369-376.
[18] Tajima K,Arai S,Ogata K,et al. Rumen bacterial community transition during adaptation to high-grain diet[J].Anaerobe,2000,6(5):273-284.
[19] Singh K M,Ahir V B, Tripathi A K,et al. Metagenomic analysis of Surti buffalo (Bubalus bubalis) rumen:A preliminary study[J].Molecular Biology Reports,2012,39(4):4841-4848.
[20] Peng S,Yin J,Liu X,et al. First insights into the microbial diversity in the omasum and reticulum of bovine using Illumina sequencing[J].Appl Genetics,2015,56(3):393-401.
[21] Stahl D A,Flesher B,Mansfield H R,et al.Use of phylogenetically based hybridization probes for studies of ruminal microbial ecology[J].Appl Environ Microbiol,1998,54(5):1079-1084.
[22] Michalet-Doreau B,Fernandez I,Peyron C,et al.Fibrolytic activities and cellulolytic bacterial community structure in the solid and liquid phases of rumen contents[J].Reprod Nutr Dev,2001,41(2):187-194.
[23] Martin C,Millet L,Fonty G,et al. Cereal supplementation modified the fibrolytic activity but not the structure of the cellulolytic bacterial community associated with rumen solid digesta[J]. Reprod Nutr Dev,2001,41(5):413-424.
[24] Weimer P J,Waghorn G C. Effect of diet on populations of three species of ruminal cellulolytic bacteria in lactating dairy cows[J].J Dairy Sci Jan,1999,82(1):122-134.
[25] Krause D O,Russell J B. An rRNA approach for assessing the role of obligate amino acid-fermenting bacteria in ruminal amino acid degradation[J].Appl Environ Microbiol,1996,62(3):815-821.
[26] Collings G F,Yokoyama M T.Gas-liquid chromatography for evaluating polysaccharide degradation by Ruminococcus flavefaciens C94 and Bacteroides succinogenes S85[J].Appl Environ Microbiol,1980,39(3):566-571.

云南大额牛瘤胃微生物多样性分析

Diversity Analysis of Rumen Microbes in Yunnan Gayals (Bos frontalis)

PDF

可视化

摘要/Abstract

引用本文

使用本文

参考文献

相关文章 4

编辑推荐

Metrics

本文评价

[1]	潘梦, 叶健强, 康润敏, 肖璐, 叶勇刚, 于吉锋, 谢晶, 曹冶, 李兴玉, 林毅, 魏甬. 宏基因组法研究不同堆肥处理下猪粪微生物动态结构特征[J]. 中国畜牧兽医, 2021, 48(7): 2671-2684.
[2]	罗佳捷;李丽立;张彬. T-RFLP技术及其在微生物群落结构研究中的应用[J]. , 2009, 36(7): 75-78.
[3]	刘开朗;王加启;卜登攀;李旦;于萍;赵圣国;奚晓琦. 2007~2008年国际反刍动物营养研究进展 Ⅰ.瘤胃微生物多样性和功能[J]. , 2009, 36(1): 5-11.
[4]	王桂军;魏建忠;李郁. 肠道共生微生物群落与家禽健康[J]. , 2007, 34(2): 153-155.