Analysis of rumen bacterial diversity of goat by denaturing gradient gel electrophoresis and 16S rDNA sequencing

Diversity of rumen bacteria of the rumen content of Chinese white goats was analyzed by PCR amplification, denaturing gradient gel electrophoresis (DGGE) and sequencing of 16S rDNA clone libraries. DNA was extracted from rumen contents of goats fed two diets with and without the addition of daidzein. The V6-V8 region of 16S rDNA of bacteria was amplified and the amplicons were then separated based on a linear gradient of denaturants in DGGE, a fingerprinting technique. A clone library was created from complete 16S rDNA. From the library, 16 clones had their V6-V8 regions matched predominant bands on the DGGE gel and their 16S rDNAs were then sequenced and subjected to an online similarity search. Five clones showed their similarities with database sequences over 97%, with one sequence similar to Prevotella sp., the rest were similar to those unidentified rumen bacteria. From the library, eight clones with similarities in the range of 90%～96% and the remaining three clones were less than 90%.