Abstract：In order to obtain high quality genomic DNA of rumen microbes in goats(Capra hircus) and analyze the microbial diversity in the rumen, 6 kinds of DNA extraction methods, including bead mill+Tris-Phenol method, bead mill+Sodium dodecyl sulfate (SDS) method, bead mill+SDS/Guanidine thiocyanate (GITC) method, bead mill+SDS/NH4Ac method, bead mill+SDS/GITC/NH4Ac method and SDS/GITC methods, were used to extract microbial genomic DNA of goats in the present research. These extraction methods were compared through measuring DNA concentration and purity, polymerase chain reaction(PCR), denaturing gradient gel electrophoresis(DGGE) technique to find the suitable method for extracting microbial genomic DNA in the rumen of goats. Results showed that microbial genomic DNA extracted by using bead mill plus sodium dodecyl sulfate/guandine thiocyanate/ammonium acetate method had better purity and the concentration of it was 96.4 ng/μL. Meanwhile, ruminal bacterial and methanogenic 16S rDNA was amplified simultaneously, and the highest 16S rDNA diversity indexes of ruminal bacteria and methanogen were found when using this method. Therefore, bead mill plus sodium dodecyl sulfate/guandine thiocyanate/ammonium acetate method is more suitable for the subsequent molecular biology research of ruminal microflora.
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