Molecular Biology Reports

, Volume 35, Issue 2, pp 265–274

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

  • Weidong Deng
  • Dongmei Xi
  • Huaming Mao
  • Metha Wanapat
Article

DOI: 10.1007/s11033-007-9079-1

Cite this article as:
Deng, W., Xi, D., Mao, H. et al. Mol Biol Rep (2008) 35: 265. doi:10.1007/s11033-007-9079-1

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.

Keywords

Rumen microbes16S/18S rRNA/rDNAHybridizationPCRFingerprint techniquesClone libraries

Copyright information

© Springer Science+Business Media B.V. 2007

Authors and Affiliations

  • Weidong Deng
    • 1
    • 2
  • Dongmei Xi
    • 1
  • Huaming Mao
    • 1
  • Metha Wanapat
    • 2
  1. 1.Yunnan Provincial Laboratory of Animal Nutrition and Feed Science, Faculty of Animal ScienceYunnan Agricultural UniversityKunmingP. R. China
  2. 2.Department of Animal Science, Faculty of AgricultureKhon Kaen UniversityKhon KaenThailand