133
Views
9
CrossRef citations to date
0
Altmetric
Articles

Description of the structural diversity of rumen microbial communities in vitro using single-strand conformation polymorphism profiles

, , , &
Pages 454-467 | Received 16 May 2008, Accepted 22 Aug 2008, Published online: 18 Nov 2008

References

  • Amann , R I , Ludwig , W and Schleifer , K-H. 1995 . Phylogenetic identification and in situ detection of individual microbial cells without cultivation . Microbiol Rev. , 59 : 143 – 169 .
  • Anderson , M J . 2001 . A new method for non-parametric multivariate analysis of variance . Aust Ecol. , 26 : 32 – 46 .
  • Anderson , M J . 2005 . PERMANOVA: a FORTRAN computer program for permutational multivariate analysis of variance Department of Statistics, University of Auckland, New Zealand
  • Anderson , M J and Robinson , J . 2003 . Generalised discriminant analysis based on distances . Aust NZ J Stat. , 45 : 301 – 318 .
  • Bassam , B J , Caetano-Anollés , G and Gresshoff , P M . 1991 . Fast and sensitive silver staining of DNA in polyacrylamide gels . Anal Biochem. , 196 : 80 – 83 .
  • Boguhn , J . 2004 . In vitro-Untersuchungen zum Einfluss der Rationszusammensetzung auf die Synthese und das Aminosäurenmuster des mikrobiellen Proteins im Pansen [Dissertation] , [Halle Saale] : Martin-Luther-Universität .
  • Boguhn , J , Kluth , H and Rodehutscord , M . 2006a . Effect of total mixed ration composition on fermentation and efficiency of ruminal microbial crude protein synthesis in vitro . J Dairy Sci. , 89 : 1580 – 1591 .
  • Boguhn , J , Kluth , H and Rodehutscord , M . 2006b . Effect of total mixed ration composition on amino acid profiles of different fractions of ruminal microbes in vitro . J Dairy Sci. , 89 : 1592 – 1603 .
  • Brandt , M and Rohr , K . 1981 . Beiträge zur Quantifizierung der N-Umsetzungen in den Vormägen von Milchkühen 1. Mitteilung: Bestimmung des Mikrobenstickstoffs im Duodenalchymus mit Hilfe von 15N . Z Tierphysiol Tierernährg Futtermittelkd. , 46 : 39 – 48 .
  • Bryant , M P and Burkey , L A . 1953 . Numbers and some predominant groups of bacteria in the rumen of cows fed different rations . J Dairy Sci. , 36 : 218 – 224 .
  • Cheng , K-J and McAllister , T A . 1997 . “ The rumen microbial ecosystem ” . In Chapter 12, Compartmentation in the rumen , Edited by: Hobson , P N and Stewart , C S . 492 – 521 . London : Blackie Academic and Professional .
  • Clarke , K R . 1993 . Non-parametric multivariate analyses of changes in community structure . Aust J Ecol. , 18 : 117 – 143 .
  • Clarke , K R and Green , R H . 1988 . Statistical design and analysis for a ‘biological effects’ study . Mar Ecol – Progress Series. , 46 : 213 – 226 .
  • Czerkawski , J W and Breckenridge , G . 1977 . Design and development of a long-term rumen simulation technique (Rusitec) . Brit J Nutr. , 38 : 371 – 384 .
  • Czerkawski , J W and Breckenridge , G . 1978 . Use of the Rumen Simulation Technique (Rusitec) to study the distribution of microbial matter in the solid and liquid phases of the reaction mixture; sequestration of micro-organisms . Proc Nutr Soc. , 37 : 70A
  • Dehority , B A and Orpin , C G . 1997 . “ Development of, and natural fluctuations in, rumen microbial populations ” . In The rumen microbial ecosystem , Edited by: Hobson , P N and Stewart , C S . 196 – 245 . London : Blackie Academic & Professional .
  • Dohrmann , A B and Tebbe , C C . 2004 . “ Microbial community analysis by PCR-single-strand conformation polymorphism (PCR-SSCP) ” . In Molecular microbial ecology manual 1 , Edited by: Kowalchuk , G A , de Bruijn , F J , Head , I M , Akkermans , A DL and van Elsas , J D . 809 – 838 . Dordrecht : Kluwer Academic Publishers .
  • Farrelly , V , Rainey , F A and Stackebrandt , E . 1995 . Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species . Appl Environ Microbiol. , 61 : 2798 – 2801 .
  • Ferguson , R L , Buckley , E N and Palumbo , A V . 1984 . Response of marine bacterioplankton to differential filtration and confinement . Appl Environ Microbiol. , 47 : 49 – 55 .
  • Firkins , J L and Yu , Z . 2006 . “ Characterisation and quantification of the microbial populations of the rumen ” . In Ruminant physiology, digestion, metabolism and impact of nutrition on gene expression, immunology and stress , Edited by: Sejrsen , K , Hvelplund , T and Nielsen , M O . 19 – 54 . Wageningen : Academic Publishers .
  • Gizzi , G , Zanchi , R and Sciaraffia , F . 1998 . Comparison of microbiological and fermentation parameters obtained with an improved rumen in vitro technique with those obtained in vivo . Anim Feed Sci Technol. , 73 : 291 – 305 .
  • Großkopf , R , Janssen , P H and Liesack , W . 1998 . Diversity and structure of the methanogenic community in anoxic rice paddy soil microcosms as examined by ultivation and direct 16S rRNA gene sequence retrieval . Appl Environ Microbiol. , 64 : 960 – 969 .
  • Hammer , Ø , Harper , D AT and Ryan , P D . 2001 . PAST: Paleontological statistics software package for education and data analysis . Palaeontol Electronica. , 4 : 1 – 9 .
  • Koch , M , Strobel , E , Tebbe , C C , Heritage , J , Breves , G and Huber , K . 2006 . Transgenic maize in the presence of ampicillin modifies the metabolic profile and microbial population structure of bovine rumen fluid in vitro . Brit J Nutr. , 96 : 820 – 829 .
  • Korhonen , M , Ahvenjärvi , S , Vanhatalo , A and Huhtanen , P . 2002 . Supplementing barley or rapeseed meal to dairy cows fed grass-red clover silage: II. Amino acid profile of microbial fractions . J Anim Sci. , 80 : 2188 – 2196 .
  • Krave , A S , Lin , B , Braster , M , Laverman , A M , van Straalen , N M , Röling , W FM and Van Verseveld , H W . 2002 . Stratification and seasonal stability of diverse bacterial communities in a Pinus merkusii (pine) forest soil in central Java, Indonesia . Environ Microbiol. , 4 : 361 – 373 .
  • Kruskal , J B . 1964 . Nonmetric multidimensional scaling: A numerical method . Psychometrika. , 29 : 115 – 129 .
  • Lane , D J . 1991 . “ Nucleic acid techniques in bacterial systematics ” . In 16S/23S rRNA Sequencing , Edited by: Stackebrandt , E and Goodfellow , M . 115 – 175 . Chichester , , UK : Wiley Intersience Publications .
  • Legendre , P and Legendre , L . 2006 . Numerical ecology , 2. Engl. ed., reprinted , Amsterdam : Elsevier .
  • Ludwig , W , Strunk , O , Westram , R , Richter , L , Meier , H , Yadhukumar, Buchner , A , Lai , T , Steppi , S , Jobb , G , Förster , W , Brettske , I , Gerber , S , Ginhart , A W , Gross , O , Grumann , S , Hermann , S , Jost , R , König , A , Liss , T , Lüßmann , R , May , M , Nonhoff , B , Reichel , B , Strehlow , R , Stamatakis , A , Stuckmann , N , Vilbig , A , Lenke , M , Ludwig , T , Bode , A and Schleifer , K-H . 2004 . ARB: a software environment for sequence data . Nuc Acids Res. , 32 : 1363 – 1371 .
  • Mathieu-Daudé , F , Cheng , R , Welsh , J and McClelland , M . 1996 . Screening of differentially amplified cDNA products from RNA arbitrarily primed PCR fingerprints using single strand conformation polymorphism (SSCP) gels . Nucleic Acids Res. , 24 : 1504 – 1507 .
  • Minato , H and Suto , T . 1978 . Technique for fractionation of bacteria in rumen microbial ecosystem. II. Attachment of bacteria isolated from bovine rumen to cellulose powder in vitro and elution of bacteria attached therefrom . J Gen Appl Microbiol. , 24 : 1 – 16 .
  • Muyzer , G , De Waal , E C and Uitierlinden , A G . 1993 . Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA . Appl Environ Microbiol. , 59 : 695 – 700 .
  • Olsen , G J , Lane , D J , Giovannoni , S J and Pace , N R . 1986 . Microbial ecology and evolution: A ribosomal RNA approach . Annu Rev Microbiol. , 40 : 337 – 365 .
  • Olsen , G J , Overbeek , R , Larsen , N , Marsh , T L , McCaughey , M J , Maciukenas , M A , Kuan , W-M , Macke , T J , Xing , Y and Woese , C R . 1992 . The ribosomal database project . Nucleic Acids Res. , 20 ( suppl. ) : 2199 – 2200 .
  • Prevot , S , Senaud , J , Bohatier , J and Prensier , G . 1994 . Variation in the composition of the ruminal bacterial microflora during the adaptation phase in an artificial fermentor (Rusitec) . Zoolog Sci (Tokyo). , 11 : 871 – 878 .
  • Ranilla , M J and Carro , M D . 2003 . Diet and procedures used to detach particle-associated microbes from ruminal digesta influence chemical composition of microbes and estimation of microbial growth in Rusitec fermenters . J Anim Sci. , 81 : 537 – 544 .
  • Reysenbach , A-L , Giver , L J , Wickham , G S and Pace , N R . 1992 . Differential amplification of rRNA genes by polymerase chain reaction . Appl Environ Microbiol. , 58 : 3417 – 3418 .
  • Rodríguez , C A , González , J , Alvir , M R , Repetto , J L , Centeno , C and Lamrani , F . 2000 . Composition of bacteria harvested from the liquid and solid fractions of the rumen of sheep as influenced by feed intake . Brit J Nutr. , 84 : 369 – 376 .
  • Schwieger , F and Tebbe , C C . 1998 . A new approach to utilize PCR – single-strand-conformation polymorphism for 16S rRNA gene-based microbial community analysis . Appl Environ Microbiol. , 64 : 4870 – 4876 .
  • Stahl , D A and Amann , R I . 1991 . “ Nucleic acid techniques in bacterial systematics ” . In Development and application of nucleic acid probes , Edited by: Stackrandt , E and Goodfellow , M . 205 – 248 . New York : John Wiley and Sons Ltd. .
  • Stahl , D A , Flesher , B , Mansfield , H R and Montgomery , L . 1988 . Use of phylogenetically based hybridization probes for studies of ruminal microbial ecology . Appl Environ Microbiol. , 54 : 1079 – 1084 .
  • Strobel , E , Seeling , K and Tebbe , C C . 2008 . Diversity responses of rumen microbial communities to Fusarium-contaminated feed, evaluated with rumen simulating technology (Rusitec) . Environ Microbiol. , 10 : 483 – 496 .
  • Strobel , E , Wesolowski , J , Flachowsky , G and Tebbe , C C . 2004 . Genetic profiles of rumen microbial communities: A cultivation independent technique to study the effect of feeding . Proc Soc Nutr Physiol. , 13 : 81
  • von Wintzingerode , F , Gobel , U B and Stackebrandt , E . 1997 . Determination of microbial diversity in environmental samples: Pitfalls of PCR-based rRNA analysis . FEMS Microbiol Rev. , 21 : 213 – 229 .
  • van Verseveld , H W and Röling , W FM . 2004 . “ Cluster analysis and statistical comparison of molecular community profile data ” . In Molecular microbial ecology manual 2 , Edited by: Kowalchuk , G A , de Bruijn , F J , Head , I M , Akkermans , A DL and van Elsas , J D . 1373 – 1396 . Dordrecht : Kluwer Academic Publishers .
  • Wallace , R J . 1994 . Ruminal microbiology, biotechnology, and ruminant nutrition: Progress and problems . J Anim Sci. , 72 : 2992 – 3003 .
  • Weisburg , W G , Barns , S M , Pelletier , D A and Lane , D J . 1991 . 16S ribosomal DNA amplification for phylogenetic study . J Bacteriol. , 173 : 697 – 703 .
  • Whiteford , M F , Forster , R J , Beard , C E , Gong , J and Teather , R M . 1998 . Phylogenetic analysis of rumen bacteria by comparative sequence analysis of cloned 16S rRNA genes . Anaerobe. , 4 : 153 – 163 .

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.