[Use of rpoB and 16S rDNA genes to analyze rumen bacterial diversity of goat using PCR and DGGE].
DNA extraction from the rumen of three species of goat (boer goat, Nanjiang yellow goat, Inner Mongolia cashmere goat) was followed by Polymerase Chain Reaction (PCR) amplification of the beta subunit of the RNA polymerase (rpoB) and 16S rDNA genes. PCR products were compared by Denaturing Gradient Gel Electrophoresis (DGGE) to compare the predominant bacterial community structure. The results showed the rpoB DGGE profiles comprised fewer bands than those of 16S rDNA profiles and were easier to analyze. The gene for rpo B is a single copy gene unlike 16S rDNA. So using the rpoB gene offeres a better alternative to the commonly used 16S rRNA gene for microbial community analyses based on DGGE. The bacteria community structure of different goats were similar to each other. The similarities within species were noticeably higher than that between species. Goat species were found to influence the rumen microbe community. Phylogenetic and sequence similarity analyses of the resultant 14 clone sequences in16S rDNA DGGE libraries revealed that 4 clone show similarity over 97% with that of database sequences, while the rest present similarity in a range of 89%-96%, and 13 clone of all were similar to those unidentified rumen bacteria. These results suggest that DGGE followed by clone technique is a practicable protocol to research the complex community of rumen microbe.
Shi
Peng-jun
PJ
Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China. pengjunshi321@yahoo.com.cn
Bai
Ying-guo
YG
Yuan
Tie-zheng
TZ
Yao
Bin
B
Fan
Yun-liu
YL
D000818:Animals; D001419:Bacteria / Q000145:classification* / Q000235:genetics; D016172:DNA Fingerprinting; D012321:DNA-Directed RNA Polymerases / Q000235:genetics*; D004591:Electrophoresis, Polyacrylamide Gel; D006041:Goats / Q000382:microbiology*; D016133:Polymerase Chain Reaction / Q000379:methods*; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D012417:Rumen / Q000382:microbiology*
D012336:RNA, Ribosomal, 16S; D012321:DNA-Directed RNA Polymerases