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The use of molecular techniques based on ribosomal RNA and DNA for rumen microbial ecosystem studies: a review

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Abstract

This paper analyses the research progress in the use of molecular techniques based on ribosomal RNA and DNA (rRNA/rDNA) for rumen microbial ecosystem since first literature by Stahl et al. (1988). Because rumen microbial populations could be under-estimated by adopting the traditional techniques such as roll-tube technique or most-probable-number estimates, modern molecular techniques based on 16S/18S rRNA/rDNA can be used to more accurately provide molecular characterization, microbe populations and classification scheme than traditional methods. Phylogenetic-group-specific probes can be used to hybridize samples for detecting and quantifying of rumen microbes. But, competitive-PCR and real-time PCR can more sensitively quantify rumen microbes than hybridization. Molecular fingerprinting techniques including both denaturing gradient gel electrophoresis (DGGE), temperature gradient gel electrophoresis (TGGE) and restriction fragment length polymorphisms (RFLP) can used to explore diversity of bacteria, protozoa and fungi in the rumen ecosystem. By constructing clone libraries of 16S/18S rRNA/rDNA of rumen microbes, more new microbes can be discovered and identified. For fungi, internal transcribed spacers (ITS) of fungi are better than 18S rRNA/rDNA for discriminating operational taxonomic units. In conclusion, 16S/18S rRNA/rDNA procedures have been used with success in rumen microbes and are quickly gaining acceptance for studying rumen microbial ecosystem, and will become useful methods for rumen ecology research. However, molecular techniques based on 16S/18S rRNA/rDNA don’t preclude classical and traditional microbiological techniques. It should used together to acquire accurate and satisfactory results.

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References

  • Amann RI, Lin C, Key R, Montgomergy L, Stahl DA (1992) Diversity among Fibrobacter isolates: towards a phylogenetic classification. Syst Appl Microbiol 15:23–31

    Google Scholar 

  • Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143–169

    PubMed  CAS  Google Scholar 

  • An DD, Dong XZ, Dong ZY (2005) Prokaryote diversity in the rumen of yak (Bos grunniens) and Jinnan cattle (Bos taurus) estimated by 16S rDNA homology analyses. Anaerobe 4:207–215

    Article  CAS  Google Scholar 

  • Attwood GT, Klieve AV, Ouwerkerk D, Patel BK (1998) Ammonia-hyperproducing bacteria from New Zealand ruminants. Appl Environ Microbiol 64:1796–1804

    PubMed  CAS  Google Scholar 

  • Avgustin G, Wright F, Flint HJ (1994) Genetic diversity and phylogenetic relationships among strains of Prevotella (Bacteroides) ruminicola from the rumen. Int J Syst Bact 44:246–255

    Article  CAS  Google Scholar 

  • Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL (2004) GenBank: update. Nucleic Acids Res 32:D23–D26

    Article  PubMed  CAS  Google Scholar 

  • Briesacher SL, May T, Grigsby KN, Kerley MS, Anthony RV, Paterson JA (1992) Use of DNA probes to monitor nutritional effects on ruminal prokaryotes and Fibrobacter succinogenes S85. J Anim Sci 70:289–295

    PubMed  CAS  Google Scholar 

  • Brookman JL, Mennim G, Trinci AP, Theodorou MK, Tuckwell DS (2000) Identification and characterization of anaerobic gut fungi using molecular methodologies based on ribosomal ITS1 and 18S rRNA. Microbiology 146(Pt 2):393–403

    PubMed  CAS  Google Scholar 

  • Cann IKO, Kocherginskaya SA, White BA (1996) Denaturing gradient gel eletrophoresis analysis of polymerase chain-reaction amplified genes coding for 16S rRNAs from ruminal fibrolytic bacteria. Proceeding of Japanese Society of Rumen Metabolism Physiology 7:10–18

    Google Scholar 

  • Chen YC, Hseu RS, Cheng KJ (2003) The genetic similarity of different generations of Neocallimastix frontalis SK. FEMS Microbiol Lett 221:227–231

    Article  PubMed  CAS  Google Scholar 

  • Dangler CA (1996) Nucleic acid analysis: principle and bioapplication. Wiley-Liss, Inc

  • Dehority BA, Tirabasso PA, Grifo AP (1989) Most-probable-number procedures for enumerating ruminal bacteria, including the simultaneous estimation of total and cellulolytic numbers in one medium. Appl Environ Microbiol 55:2789–2792

    PubMed  CAS  Google Scholar 

  • Delong EF, Wickham GS, Pace NP (1989) Phylogenetic stains: ribosomal RNA-based probes for the identification of single cells. Science 243:1360–1363

    Article  PubMed  CAS  Google Scholar 

  • Deng WD, Wanapat M, Ma SC, Chen J, Xi DM, He TB, Yang ZF, Mao HM (2007) Phylogenetic analysis of 16S rDNA sequences manifest rumen bacterial diversity in Gayal (Bos frontalis) fed fresh bamboo leaves and twigs (Sinarumdinaria). Asian-Aust J Anim Sci (in press)

  • Farrelly V, Rainey FA, 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

    PubMed  CAS  Google Scholar 

  • Felske A, Akkermans ADL, De Vos WM (1998) Quantification of 16S rRNAs in complex bacterial communities by multiple competitive reverse transcription-PCR in temperature gradient gel electrophoresis fingerprints. Appl Environ Microbiol 64:4581–4587

    PubMed  CAS  Google Scholar 

  • Forster RJ, Gong JH, Teather RM (1997) Group-Specific 16S rRNA hybridization probes for determinative and community structure studies of Butyrivibrio fibrisolvens in the rumen. Appl Environ Microbiol 63:1256–1260

    PubMed  CAS  Google Scholar 

  • Garcia-Martinez J, Acinas SG, Anton AI, Rodriguez-Valera F (1999) Use of the 16S-23S ribosomal genes spacer region in studies of prokaryotic diversity. J Microbiol Methods 36:55–64

    Article  PubMed  CAS  Google Scholar 

  • Gerbi SA (1985) Evolution of ribosomal DNA. In: MacIntyre RJ (ed). Molecular evolutionary genetics. Plenum, New York, pp 419–517

    Google Scholar 

  • Higuchi R, Fockler C, Dollinger G, Watson R (1993) Kinetic PCR analysis: real-time monitoring of DNA amplification reactions. Biotech 11:1026–1030

    Article  CAS  Google Scholar 

  • Holland PM, Abramson RD, Watson R, Gelfand DH (1991) Detection of specific polymerase chain reaction product by utilizing the 5’ to 3’ exonuclease activity of Thermus aquaticus DNA polymerase. Proc Natl Acad Sci USA 88:7276–7280

    Article  PubMed  CAS  Google Scholar 

  • Hungate RE (1969) A roll tube method for cultivation of strict anaerobes. In: Norris JR, Ribbons DW (eds) Methods in microbiology, vol 3B. Academic Press, London and New York, pp 117–132

    Google Scholar 

  • Jarvis GN, Kurtovic A, Hay AG, Russell JB (2001) The physiological and genetic diversity of bovine Streptococcus bovis strains. FEMS Microbiol Ecol 35:49–56

    PubMed  CAS  Google Scholar 

  • Jarvis GN, Strompl C, Burgess DM, Skillman LC, Moore ER, Joblin KN (2000) Isolation and identification of ruminal methanogens from grazing cattle. Curr Microbiol 40:327–332

    Article  PubMed  CAS  Google Scholar 

  • Kane MD, Poulsen LK, Stahl DA (1993) Monitoring the enrichment and isolation of sulfate-reducing bacteria by using oligonucleotide hybridization probes designed from environmentally derived 16S rRNA sequences. Appl Environ Microbiol 59:682–686

    PubMed  CAS  Google Scholar 

  • Karnati SKR, Yu Z, Sylvester JT, Dehority BA, Morrison M, Firkins JL (2003) Technical note: Specific PCR amplification of protozoal 18S rDNA sequences from DNA extracted from ruminal samples of cows. J Anim Sci 81:812–815

    PubMed  CAS  Google Scholar 

  • Kauppinen J, Mantyjarvi R, Katila ML (1999) Mycobacterium malmoense-specific nested PCR based on a conserved sequence detected in random amplified polymorphic DNA fingerprints. J Clin Microbiol 37:1454–1458

    PubMed  CAS  Google Scholar 

  • Klieve AV, Hennessey D, Ouwerkerk D, Forster RJ, Mackie RI, Attwood GT (2003) Establishing populations of Megasphaera elsdenii YE34 and Butyrivibrio fibrisolvens YE44 in the rumen of cattle fed high grain diets. J Appl Microbiol 95:621–630

    Article  PubMed  CAS  Google Scholar 

  • Klieve AV, Heck GL, Prince MA, Shu Q (1999) Genetic homogenity and phage suspectibility of ruminal strains of Streptococcus bovis isolated in Australia. Lett Appl Microbiol 29:108–112

    Article  PubMed  CAS  Google Scholar 

  • Kobayashi Y, Forster RJ, Teather RM (2000) Development of a competitive polymerase chain reaction assay for the ruminal bacterium Butyrivibrio fibrisolvens OB156 and its use for tracking an OB156-derived recombinant. FEMS Microbiol Lett 188:185–190

    Article  PubMed  CAS  Google Scholar 

  • Kocherginskaya SA, Aminov RI, White BA (2001) Analysis of the rumen bacterial diversity under two different diet conditions using denaturing gradient gel electrophoresis, random sequencing, and statistical ecology approaches. Anaerobe 7:119–134

    Article  CAS  Google Scholar 

  • Koike S, Kobayashi Y (2001) Development and use of competitive PCR assays for the rumen cellulolytic bacteria: Fibrobacter succinogenes, Ruminococcus albus and Ruminococcus flavefaciens. FEMS Microbiol Lett 204:361–366

    Article  PubMed  CAS  Google Scholar 

  • Koike S, Pan J, Kobayashi Y, Tanaka K (2003a) Kinetics of in sacco fiber-attachment of representative ruminal cellulolytic bacteria monitored by competitive PCR. J Dairy Sci 86:1429–1435

    Article  PubMed  CAS  Google Scholar 

  • Koike S, Yoshitani S, Kobayashi Y, Tanaka K (2003b) Phylogenetic analysis of fiber-associated rumen bacterial community and PCR detection of uncultured bacteria. FEMS Microbiol Lett 229:23–30

    Article  PubMed  CAS  Google Scholar 

  • Konstantinov SR, Zhu WY, Williams BA, Tamminga S, de Vos WM, Akkermans ADL (2003). Effect of fermentable carbohydrates on piglet faecal bacterial communities as revealed by denaturing gradient gel electrophoresis analysis of 16S ribosomal DNA. FEMS Microbiol Ecol 43:225–235

    Article  CAS  PubMed  Google Scholar 

  • Krause DO, Russell JB (1996). How many ruminal bacteria are there? J Dairy Sci 79:1467–1475

    Article  PubMed  CAS  Google Scholar 

  • Krause DO, Darlymple BP, Smith WJ, Mackie RI, McSweeney CS (1999) 16S rDNA sequencing of Ruminococcus albus and Ruminococcus flavefaciens: design of a signature probe and its application in adult sheep. Microbiology 145:1787–1807

    Google Scholar 

  • Krause DO, Denman SE, Mackie RI, Morrison M, Rae AL, Attwood GT, McSweeney CS (2003) Opportunities to improve fiber degradation in the rumen: microbiology, ecology, and genomics. FEMS Microbiol Rev 27:663–693

    Article  PubMed  CAS  Google Scholar 

  • Lee DH, Zo YG, Kim SJ (1996) Nonradioactive method to study genetic profiles of natural bacterial communities by PCR-single-strand-conformation polymorphism. Appl Environ Microbiol 62:3112–3120

    PubMed  CAS  Google Scholar 

  • Li J, Heath IB (1992) The phylogenetic relationships of the anaerobic chytridiomycetous gut fungi (Neocallimasticaceae) and the Chytridiomycota. I. Cladistic analysis of rRNA sequences. Can J Bot 70:1738–1746

    Article  Google Scholar 

  • Mackie RI, Aminov RI, White BA, McSweeney CS (2000) Molecular ecology and diversity in gut microbial ecosystems. In: Cronjé PB (ed) Ruminant physiology: digestion, metabolism, growth and reproduction. CAB International, London, UK, pp 61–77

    Google Scholar 

  • Mackie RI, Aminov RI, Hu W, Klieve AV, Ouwerkerk D, Sundset MA, Kamagata Y (2003) Ecology of uncultivated Oscillospira species in the rumen of cattle, sheep, and reindeer as assessed by microscopy and molecular approaches. Appl Environ Microbiol 69:6808–6815

    Article  PubMed  CAS  Google Scholar 

  • Madden TL, Tatusov RL, Zhang J (1996) Application of network BLAST server. Methods Enzymol 266:131–141

    Article  PubMed  CAS  Google Scholar 

  • Maidak BL, Cole JR, Lilburn TG, Parker CT Jr, Saxman PR, Farris RJ, Garrity GM, Olsen GJ, Schmidt TM Tiedje JM (2001) The RDP-II (Ribosomal Database Project). Nucleic Acids Res 29:173–174

  • Mao SY, Zhang G, Zhu WY (2007) Effect of disodium fumarate on in vitro rumen fermentation of different substrates and rumen bacterial communities as revealed by denaturing gradient gel electrophoresis analysis of 16s ribosomal DNA. Asian-Aust J Anim Sci 20:543–549

    CAS  Google Scholar 

  • McCracken VJ, Simpson JM, Mackie RI, Gaskins HR (2001) Molecular ecological analysis of dietary and antibiotic-induced alterations of the mouse intestinal microbiota. J Nutr 131:1862–1870

    PubMed  CAS  Google Scholar 

  • Michalet-Doreau B, Fernandez I, Fonty G (2002) A comparison of enzymatic and molecular approaches to characterize the cellulolytic microbial ecosystems of the rumen and the cecum. J Anim Sci 80:790–796

    PubMed  CAS  Google Scholar 

  • Michalet-Doreau B, Fernandez I, Peyron C, Millet L (2001) Fibrolytic activities and cellulolytic bacterial community structure in the solid and liquid phases of rumen contents. Reprod Nutr Dev 41:187–194

    Article  PubMed  CAS  Google Scholar 

  • Miron J, Ben-Ghedalia D, Morrison M (2001) Invited review: adhesion mechanisms of rumen cellulolytic bacteria. J Dairy Sci 84:1294–1309

    PubMed  CAS  Google Scholar 

  • Moeseneder MM, Arrieta JM, Muyzer G, Winter C, Herndl GJ (1999) Optimization of terminal-restriction fragment length polymorphism analysis for complex marine bacterioplankton communities and comparison with denaturing gradient gel electrophoresis. Appl Environ Microbiol 65:3518–3525

    PubMed  CAS  Google Scholar 

  • Muyzer G (1999) DGGE/TGGE a method for identifying genes from natural ecosystems. Curr Opin Microbiol 2:317–322

    Article  PubMed  CAS  Google Scholar 

  • Muyzer G, Smalla K (1998) Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel eletrophoresis (TGGE) in microbial ecology. Antonie van Leeuwenhoek 73:127–141

    Article  PubMed  CAS  Google Scholar 

  • Muyzer G, De Waal EC, Uitterlinden AG (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

    PubMed  CAS  Google Scholar 

  • Nelson KE, Zinder SH, Hance I, Burr P, Odongo D, Wasawo D, Odenyo A, Bishop R (2003) Phylogenetic analysis of the microbial populations in the wild herbivore gastrointestinal tract: insights into an unexplored niche. Environ Microbiol 5:1212–1220

    Article  PubMed  Google Scholar 

  • Nicolaisen MH, Ramsing NB (2002) Denaturing gradient gel electrophoresis (DGGE) approaches to study the diversity of ammonia-oxidizing bacteria. J Microbiol Methods 50:189–203

    Article  PubMed  CAS  Google Scholar 

  • Nikolausz M, Sipos R, Révész S, Székely A, Márialigeti K (2005) Observation of bias associated with re-amplification of DNA isolated from denaturing gradient gels. FEMS Microbiol Lett 2:385–390

    Article  CAS  Google Scholar 

  • Noftsger SM, St-Pierre NR, Karnati SKR, Firkins JL (2003) Effects of 2-Hydroxy-4-(methylthio) butanoic acid (HMB) on microbial growth in continuous culture. J Dairy Sci 86:2629–2636

    PubMed  CAS  Google Scholar 

  • Olsen GJ, Lane DJ, Giovannoni SJ, Pace NR, Stahl DA (1986) Microbial ecology and evolution: a ribosomal RNA approach. Annu Rev Microbiol 40:337–365

    Article  PubMed  CAS  Google Scholar 

  • Ouwerkerk D, Klieve AV, Forster RJ (2002) Enumeration of Megasphaera elsdenii in rumen contents by real-time Taq nuclease assay. J Appl Microbiol 92:753–758

    Article  PubMed  CAS  Google Scholar 

  • Ozutsumi Y, Tajima K, Takenaka A, Itabashi H (2005) The effect of protozoa on the composition of rumen bacteria in cattle using 16S rRNA gene clone libraries. Biosci Biotechnol Biochem 69:499–506

    Article  PubMed  CAS  Google Scholar 

  • Pace NR, Olsen GJ, Woese CR (1986) Ribosomal RNA phylogeny and the primary lines of evolutionary descent. Cell 45:325–326

    Article  PubMed  CAS  Google Scholar 

  • Pelandakis M, Serre S, Pernin P (2000) Analysis of the 5.8S rRNA Gene and the Internal Transcribed Spacers in Naegleria spp. and in N. fowleri. J Eukaryot Microbiol 47:116–121

    Article  PubMed  CAS  Google Scholar 

  • Raskin L, Capman WC, Sharp R, Poulson LK, Stahl DA (1997) Molecular ecology of gastrointestinal systems. In: Mackie RI, White BA, Isaacson R (ed) Gastrointestinal Microbiology II. Chapman and Hall, New York, pp 243–298

    Google Scholar 

  • Regensbogenova M, McEwan NR, Javorsky P, Kisidayova S, Michalowski T, Newbold CJ, Hackstein JHP, Pristas P (2004a). A re-appraisal of the diversity of the methanogens associated with the rumen ciliates. FEMS Microbiol Lett 238:307–313

    Article  PubMed  CAS  Google Scholar 

  • Regensbogenova M, Pristas P, Javorsky P, Der MV, Staay SY, Staay VDGW, Hackstein JH, Newbold CJ, McEwan NR (2004b) Assessment of ciliates in the sheep rumen by DGGE. Lett Appl Microbiol 39:144–147

  • Reilly K, Attwood GT (1998) Detection of Clostridium proteoclasticum and closely related strains in the rumen by competitive PCR. Appl Environ Microbiol 64:907–913

    PubMed  CAS  Google Scholar 

  • Reysenbach AL, Giver LJ, Wickham GS, Pace NR (1992) Differential amplification of rRNA genes by polymerase chain reaction. Appl Environ Microbiol 58:3417–3418

    PubMed  CAS  Google Scholar 

  • Sasaki E, Osawa R, Nishitani Y, Whiley RA (2004) ARDRA and RAPD analyses of human and animal isolates of Streptococcus gallolyticus. J Vet Med Sci 66:1467–1470

    Article  PubMed  CAS  Google Scholar 

  • Schlegel L, Grimont F, Grimont PA, Bouvet A (2003) Identification of major Streptococcal species by rrn-amplified ribosomal DNA restriction analysis. J Clin Microbiol 41:657–666

    Article  PubMed  CAS  Google Scholar 

  • Shin EC, Choi BR, Lim WJ, Hong SY, An CL, Cho KM, Kim YK, An JM, Kang JM, Lee SS, Kim H, Yun HD (2004a) Phylogenetic analysis of archaea in three fractions of cow rumen based on the 16S rDNA sequence. Anaerobe 10:313–319

    Article  PubMed  CAS  Google Scholar 

  • Shin EC, Cho KM, Lim WJ, Hong SY, An CL, Kim EJ, Kim YK, Choi BR, An JM, Kang JM, Kim H, Yun HD (2004b) Phylogenetic analysis of protozoa in the rumen contents of cow based on the 18S rDNA sequences. J Appl Microbiol 97:378–383

    Article  PubMed  CAS  Google Scholar 

  • Simpson JM, McCracken VJ, White BA, Gaskins HR, Mackie RI (1999) Application of denaturant gradient gel electrophoresis for the analysis of the porcine gastrointestinal microbiota. J Microbiol Methods 36:167–179

    Article  PubMed  CAS  Google Scholar 

  • Simpson JM, McCracken VJ, Gaskins HR, Mackie RI (2000) Denaturing gradient gel electrophoresis analysis of 16S ribosomal DNA amplicons to monitor changes in fecal bacterial populations of weaning pigs after introduction of Lactobacillus reuteri strain MM53. Appl Environ Microbiol 66:4705–4714

    Article  PubMed  CAS  Google Scholar 

  • Smith AH, Mackie RI (2004) Effect of condensed tannins on bacterial diversity and metabolic activity in the rat gastrointestinal tract. Appl Environ Microbiol 70:1104–1115

    Article  PubMed  CAS  Google Scholar 

  • Soliva CR, Meile L, Hindrichsen IK, Kreuzer M, Machmüller A (2004) Myristic acid supports the immediate inhibitory effect of lauric acid on ruminal methanogens and methane release. Anaerobe 10:269–276

    Article  PubMed  CAS  Google Scholar 

  • Stackebrandt E, Goebel BM (1994) Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44:846–847

    CAS  Google Scholar 

  • Stahl DA, Flesher B, Mansfield HR, Montgomery L (1988) Use of phylogenetically-based hybridization probes for studies of rumen microbial ecology. Appl Environ Microbiol 54:1079–1084

    PubMed  CAS  Google Scholar 

  • Sylvester JT, Karnati SKR, Yu Z, Morrison M, Firkins JL (2004) Development of an assay to quantify rumen ciliate protozoal biomass in cows using real-time PCR. J Nutr 134:3378–3384

    PubMed  CAS  Google Scholar 

  • Tajima K, Aminov RI, Nagamine T, Ogata K, Nakamura M, Matsui H, Benno Y (1999) Rumen bacterial diversity as determined by sequence analysis of 16S rDNA libraries. FEMS Microbiol Ecol 29:159–169

    Article  CAS  Google Scholar 

  • Tajima K, Arai S, Ogata K, Nagamine T, Matsui H, Nakamura M, Aminov RI, Benno Y (2000) Rumen bacterial community transition during adaptation to high-grain diet. Anaerobe 6:273–284

    Article  CAS  Google Scholar 

  • Tajima K, Nagamine T, Matsui H, Nakamura M, Aminov RI (2001b) Phylogenetic analysis of archaeal 16S rRNA libraries from the rumen suggests the existence of a novel group of archaea not associated with known methanogens. FEMS Microbiol Lett 200:67–72

    Article  PubMed  CAS  Google Scholar 

  • Tajima K, Aminov RI, Nagamine T, Matsui H, Nakamura M, Benno Y (2001a) Diet-dependent shifts in the bacterial population of the rumen revealed with real-time PCR. Appl Environ Microbiol 67:2766–2774

    Article  PubMed  CAS  Google Scholar 

  • Temmerman R, Masco L, Vanhoutte T, Huys G, Swings J (2003). Development and validation of a nested-PCR-denaturing gradient gel electrophoresis method for taxonomic characterization of bifidobacterial communities. Appl Environ Microbiol 69:6380–6385

    Article  PubMed  CAS  Google Scholar 

  • Tokura M, Chagan I, Ushida K, Kojima Y (1999) Phylogenetic study of methanogens associated with rumen ciliates. Curr Microbiol 3:123–128

    Article  Google Scholar 

  • Van Kuppeveld FJM, Van Der Logt JTM, Angulo AF, Van Zoest MJ, Quint WGV, Niesters HGM, Galama JMD, Melchers WJG (1992) Genus- and species-specific identification of mycoplasmas by 16S rRNA amplification. Appl Environ Microbiol 58:2606–2615

    PubMed  Google Scholar 

  • Van Soest PJ (1994) Nutritional ecology of the ruminant. 2nd edn. Cornell University Press, Ithaca, New York

    Google Scholar 

  • Vaughan EE, Heilig HGHJ, Zoetendal EG, Satokari R, Collins JK, Akkermans ADL, de Vos WM (1999) Molecular approaches to study probiotic bacteria. Trends Food Sci Tech 10:400–404

    Article  CAS  Google Scholar 

  • Wang RF, Cao WW, Cerniglia CE (1996) PCR detection and quantitation of predominant anaerobic bacteria in human and animal fecal samples. Appl Environ Microbiol 62:1242–1247

    PubMed  CAS  Google Scholar 

  • Weimer PJ, Waghorn GC, Odt CL, Mertens DR (1999) Effect of diet on populations of three species of ruminal cellulolytic bacteria in lactating dairy cows. J Dairy Sci 82:122–134

    Article  PubMed  CAS  Google Scholar 

  • Wheelis ML, Kandler O, Woese CR (1992) On the nature of global classification. Proc Natl Acad Sci USA 89:2930–2934

    Article  PubMed  CAS  Google Scholar 

  • Whitford MF, Forster RJ, Beard CE, Gong J, Teather RM (1998) Phylogenetic analysis of rumen bacteria by comparative sequence analysis of cloned 16S rRNA genes. Anaerobe 4:153–163

    Article  PubMed  CAS  Google Scholar 

  • Whitford MF, Teather RM, Forster RJ (2001) Phylogenetic analysis of methanogens from the bovine rumen. BMC Microbiol 1:5–10

    Article  PubMed  CAS  Google Scholar 

  • Wintzingerode FV, Göbel U, Stackebrandt E (1997) Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev 21:213–229

    Article  Google Scholar 

  • Woese CR, Kandler O, Wheelis ML (1990) Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 87:4576–4579

    Article  PubMed  CAS  Google Scholar 

  • Wright AD, Dehority BA, Lynn DH (1997) Phylogeny of the rumen ciliates Entodinium, Epidinium and Polyplastron (Litostomatea: Entodiniomorphida) inferred from small subunit ribosomal RNA sequences. J Eukaryot Microbiol 44:61–67

    Article  PubMed  CAS  Google Scholar 

  • Wright ADG, Williams AJ, Winder B, Christophersen CT, Rodgers SL, Smith KD (2004) Molecular diversity of rumen methanogens from sheep in Western Australia. Appl Environ Microbiol 70:1263–1270

    Article  PubMed  CAS  Google Scholar 

  • Yanagita K, Kamagata Y, Kawaharasaki M, Suzuki T, Nakamura Y, Minato H (2000) Phylogenetic analysis of methanogens in sheep rumen ecosystem and detection of Methanomicrobium mobile by fluorescence in situ hybridization. Biosci Biotechnol Biochem 64:1737–1742

    Article  PubMed  CAS  Google Scholar 

  • Yu ZT, Morrison M (2004) Comparisons of different hypervariable regions of rrs genes for use in fingerprinting of microbial communities by PCR-denaturing gradient gel electrophoresis. Appl Environ Microbiol 70:4800–4806

    Article  PubMed  CAS  Google Scholar 

  • Zheng D, Alm EW, Stahl DA, Raskin L (1996) Characterization of universal small-subunit rRNA hybridization probes for quantitative molecular microbial ecology studies. Appl Environ Microbiol 62:4504–4513

    PubMed  CAS  Google Scholar 

  • Zhu WY, Williams BA, Konstantinov SR, Tamminga S, De Vos WM, Akkermans ADL (2003) Analysis of 16S rDNA reveals bacterial shift during in vitro fermentation of fermentable carbohydrate using piglet faeces as inoculum. Anaerobe 9:175–180

    Article  PubMed  CAS  Google Scholar 

  • Ziemer CJ, Sharp R, Stern MD, Cotta MA, Whitehead TR, Stahl DA (2000) Comparison of microbial populations in model and natural rumens using 16S ribosomal RNA-targeted probes. Environ Microbiol 2:632–643

    Article  PubMed  CAS  Google Scholar 

  • Zoetendal EG, Akkermans AL, Devos WM (1998) Temperature gradient gel electrophoresis analysis of 16S rRNA from human fecal samples reveals stable and host-specific communities of active bacteria. Appl Environ Microbiol 64:3854–3859

    PubMed  CAS  Google Scholar 

  • Zoetendal EG, Collier CT, Koike S, Mackie RI, Gaskins HR (2004) Molecular ecological analysis of the gastrointestinal microbiota: A review. J Nutr 134:465–472

    PubMed  CAS  Google Scholar 

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Acknowledgments

The paper was supported by the Yunnan Provincial Natural Science Fund under Contract 2005C0038M and the Greater Mekong Subregion-Khon Kaen University Scholarship (GMS-KKU to Dr. Weidong Deng). The authors thank Dr. Peter Rowlinson and anonymous reviewers for comments on the manuscript.

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  1. Yunnan Provincial Laboratory of Animal Nutrition and Feed Science, Faculty of Animal Science, Yunnan Agricultural University, Kunming, 650201, P. R. China

    Weidong Deng, Dongmei Xi & Huaming Mao

  2. Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002, Thailand

    Weidong Deng & Metha Wanapat

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  1. Weidong Deng
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Correspondence to Metha Wanapat.

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Deng, W., Xi, D., Mao, H. et al. The use of molecular techniques based on ribosomal RNA and DNA for rumen microbial ecosystem studies: a review. Mol Biol Rep 35, 265–274 (2008). https://doi.org/10.1007/s11033-007-9079-1

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