Evaluation of DNA extraction methods of rumen microbial populations

The dynamism of microbial populations in the rumen has been studied with molecular methods that analyze single nucleotide polymorphisms of ribosomal RNA gene fragments (rDNA). Therefore DNA of good quality is needed for this kind of analysis. In this work we report the evaluation of four DNA extract...

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Bibliographic Details
Published in:World journal of microbiology & biotechnology 2013-02, Vol.29 (2), p.301-307
Main Authors: Villegas-Rivera, Gabriela, Vargas-Cabrera, Yevani, González-Silva, Napoleón, Aguilera-García, Florentino, Gutiérrez-Vázquez, Ernestina, Bravo-Patiño, Alejandro, Cajero-Juárez, Marcos, Baizabal-Aguirre, Víctor Manuel, Valdez-Alarcón, Juan José
Format: Article
Language:English
Subjects:
Alcohol
Analysis
Analytic Sample Preparation Methods - methods
Animals
Applied Microbiology
Bacteria - classification
Bacteria - genetics
Bacteria - isolation & purification
Biochemistry
Biomedical and Life Sciences
Biotechnology
Cattle
Deoxyribonucleic acid
DNA
DNA, Bacterial - chemistry
DNA, Bacterial - genetics
DNA, Bacterial - isolation & purification
DNA, Ribosomal - genetics
DNA, Ribosomal - isolation & purification
Entodinium caudatum
Environmental Engineering/Biotechnology
Ethanol
Eudiplodinium
Extraction
Fluid flow
Fragments
Life Sciences
Male
Methods
Microbiology
Microorganisms
Molecular Sequence Data
Original Paper
Phenols
Phylogeny
Polymorphism
Polymorphism, Single-Stranded Conformational
Populations
Protozoa
Ribonucleic acids
Rumen - microbiology
Studies
Syrups & sweeteners
Urea
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Summary:The dynamism of microbial populations in the rumen has been studied with molecular methods that analyze single nucleotide polymorphisms of ribosomal RNA gene fragments (rDNA). Therefore DNA of good quality is needed for this kind of analysis. In this work we report the evaluation of four DNA extraction protocols (mechanical lysis or chemical lysis with CTAB, ethylxanthogenate or DNAzol ® ) from ruminal fluid. The suitability of two of these protocols (mechanical lysis and DNAzol ® ) was tested on single-strand conformation polymorphism (SSCP) of rDNA of rumen microbial populations. DNAzol ® was a simple method that rendered good integrity, yield and purity. With this method, subtle changes in protozoan populations were detected in young bulls fed with slightly different formulations of a supplement of multinutritional blocks of molasses and urea. Sequences related to Eudiplodinium maggi and a non-cultured Entodiniomorphid similar to Entodinium caudatum , were related to major fluctuating populations in an SSCP assay.
ISSN:0959-3993
1573-0972
DOI:10.1007/s11274-012-1183-2