Biolog ECO 和 DGGE 数据几种分析方法的比较研究

毛如志 已出版文章查询
毛如志
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王文鹏
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李彬
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何霞红
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1云南农业大学农业生物多样性研究中心,云南昆明,650201

2宣威市农业局农技推广中心,云南宣威,655400


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PCA Principal Component Analysis 常用于Biolog ECO和DGGE数据分析,但是该方法无法正确区分不同环境微生物的多样性结构,也无法实现微生物标记的发现。为实现该功能,研究采用PCA、 PLS-DA partial least squares -discri-iminate analysis 、 PLS-EDA partial least squares-discriiminate enhance analysis 及PLS partial least squares 、 OPLS or-thogonal to partial least squares 方法对Biolog ECO和DGGE数据进行分析。结果表明DGGE数据通过PLS-EDA分析方法能区分不同环境微生物多样性的结构 PC1=16.8%采用PLS-DA分析方法,发现两个环境样品中有1个样品重合 PC1=33% PCA分析方法分离效果最差 PC1=27.1%。 Biolog ECO数据通过 PLS-EDA分析方法能区分不同环境微生物多样性的结构 PC1=25.5% PLS-DA分析方法有4个样品重合 PC1=36.3% PCA分析方法效果最差 PC1=35.1%。 Biolog ECO和DGGE数据进行PLS和OPLS分析方法筛选后,发现多个潜在的碳源及物种,可作为不同环境条件下微生物标记物。可见, PLS-EDA优于PLS-DA及PCA,是微生物研究的重要方法 PLS和OPLS分析方法中VIP vari-able important value≥1.00的条带和碳源可作为潜在的微生物标记。图7,表1,参24。

[1] Choi KH.;Dobbs FC. .Comparison of two kinds of Biolog microplates (GN and ECO) in theirability to distinguish among aquatic microbial communities[J].Journal of Microbiological Methods,1999(3):203-213.

[2] Muyzer G;Smalla K .Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in mi-crobial ecology[J].Antonie Van Leeuwenboek,1998,73(01):127-141.

[3] Muyzer G;Brinkhoff T;Nübel U.Denaturing gradient gel electrophoresis (DGGE) in microbial ecology[A].Dordrecht:Kluwer Academic Publishers,1997

[4] Christopher T. Green;Kate M. Scow .Analysis of phospholipid fatty acids (PLFA) to characterize microbial communities in aquifers[J].Hydrogeology journal,2000(1):126-141.

[5] Rondon M R;August P R;Bettermann A D et al.Cloning the soil metagenome:a strategy for accessing the genetic and functional diversity of uncultured microorganisms[J].APPLIED AND ENVIRONMENTAL MICROBIOLOGY,2000,66(06):2541-2547.

[6] Borneman J;Skroch PW;Osullivan KM;Palus JA;Rumjanek NG;Jansen .MOLECULAR MICROBIAL DIVERSITY OF AN AGRICULTURAL SOIL IN WISCONSIN[J].Applied and Environmental Microbiology,1996(6):1935-1943.

[7] LIU Bing-Ru,JIA Guo-Mei,CHEN Jian,WANG Gang.A Review of Methods for Studying Microbial Diversity in Soils[J].土壤圈(意译名),2006(01):18-24.

[8] Frosteg?rd 樻 B;Tunlio A et al.Shifts in the structure of soil microbial communities in limed forests as revealed by phospholipid fatty acid analysis[J].Soil Biology and Biochemistry,1993,25(06):723-730.

[9] Booth, S.C.;Workentine, M.L.;Wen, J.;Shaykhutdinov, R.;Vogel, H.J.;Ceri, H.;Turner, R.J.;Weljie, A.M. .Differences in metabolism between the biofilm and planktonic response to metal stress[J].Journal of proteome research,2011(7):3190-3199.

[10] Thomas Verron;Robert Sabatier;Richard Joffre .Some theoretical properties of the O-PLS method[J].Journal of Chemometrics,2004(2):62-68.

[11] Hans Stenlund;Andras Gorzsas;Per Persson;Bjorn Sundberg;Johan Trygg .Orthogonal Projections to Latent Structures Discriminant Analysis Modeling on in Situ FT-IR Spectral Imaging of Liver Tissue for Identifying Sources of Variability[J].Analytical chemistry,2008(18):6898-6906.

[12] Sylvie Chevallier;Dominique Bertrand;Achim Kohler .Application of PLS-DA in multivariate image analysis[J].Journal of Chemometrics,2006(5):221-229.

[13] Qiu, YP;Cai, GX;Su, MM;Chen, TL;Zheng, XJ;Xu, Y;Ni, Y;Zhao, AH;Xu, LX;Cai, SJ;Jia, W .Serum Metabolite Profiling of Human Colorectal Cancer Using GC-TOFMS and UPLC-QTOFMS[J].Journal of proteome research,2009(10):4844-4850.

[14] Tugizimana F;Piater L;Dubery I .Plant metabolomics:A new frontier in phytochemical analysis[J].South African Journal of Science,2013,109(5-6):1-11.

[15] Cavigelli MA;Robertson GP;Klug MJ .FATTY ACID METHYL ESTER (FAME) PROFILES AS MEASURES OF SOIL MICROBIAL COMMUNITY STRUCTURE[J].Plant and Soil,1995(1):99-113.

[16] Kirk, JL;Beaudette, LA;Hart, M;Moutoglis, P;Khironomos, JN;Lee, H;Trevors, JT .Methods of studying soil microbial diversity[J].Journal of Microbiological Methods,2004(2):169-188.

[17] 王强,戴九兰,吴大千,余悦,申天琳,王仁卿.微生物生态研究中基于BIOLOG方法的数据分析[J].生态学报,2010(03):817-823.

[18] 邢德峰,任南琪.应用DGGE研究微生物群落时的常见问题分析[J].微生物学报,2006(02):331-335.

[19] 辛亮,武传东,曲东.长期施肥对旱地土壤中氨氧化微生物丰度和分布的影响[J].西北农业学报,2012(06):41-46.

[20] Pietikainen J;Fritze H .CLEAR-CUTTING AND PRESCRIBED BURNING IN CONIFEROUS FOREST - COMPARISON OF EFFECTS ON SOIL FUNGAL AND TOTAL MICROBIAL BIOMASS, RESPIRATION ACTIVITY AND NITRIFICATION[J].Soil Biology and Biochemistry,1995(1):101-109.

[21] Frosteg?rd;Tunlid A B et al.Phospholipid fatty acid composition,biomass,and activity of microbial communities from two soil types experimentally exposed to different heavy metals[J].APPLIED AND ENVIRONMENTAL MICROBIOLOGY,1993,59(11):3605-3617.

[22] Wolfram Weckwerth .Metabolomics in systems biology[J].Annual review of plant biology,2003(0):669-689.

[23] Jacob G. Bundy;Matthew P. Davey Mark R. Viant .Environmental metabolomics: a critical review and future perspectives[J].Metabolomics: Official journal of the Metabolomic Society,2009(1):3-21.

[24] Xia J G;Mandal R;Sinelnikov I V et al.MetaboAnalyst 2.0-a comprehensive server for metabolomic data analysis[J].Nucleic acids re-search,2012,40(W1):W127-W133.


DOI: http://dx.doi.org/10.11689/j.issn.2095-2961.2014.02.005

语种: 中文   

基金973项目(2011CB100400)

关键词Biolog ECO DGGE 数据 PCA PLS-DA PLS-EDA PLS OPLS


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