Poster Presentations

Session Title: The Animal Microbiome
Presentation Date: Monday, August 18, 2008
Poster Board Number: 0374

COMPARATIVE RNA BASED ANALYSIS OF THE MICROBIAL DIVERSITY IN THE RUMEN SUGGESTS THAT THE PROTEOBACTERIA ARE A HIGHLY ACTIVE GROUP

S. Kang¹, S.E. Denman¹, M. Morrison¹, Z. Yu², C.S. McSweeney^1
1CSIRO, Livestock Industry, Brisbane, Australia, ²Ohio State University, Animal Science, Columbus, United States of America

Diversity of microbial communities is commonly ascertained by targeting total community 16S rDNA. By focusing on rRNA we gain an additional insight into the contributions that some bacteria play in these communities. Here we compare total rumen microbial diversity from rDNA and rRNA derived material through hybridization to a custom microarray and construction of an rRNA based clone library. Bacterial DNA and RNA from cattle rumen was extracted and amplified using bacterial primers with the modification of a T7 promoter sequence attached to the reverse primer (27F - 1492_T7R) followed by cRNA synthesis and labelling with Cy5. Microbial diversity and abundance were observed by hybridization to a 16S rDNA based custom microarray. Phylogenetic libraries were generated from rRNA and compared with previously generated rDNA based phylogenetic data. Within the rumen microbial community the Proteobacteria group has been reported to be less than 2% of total bacterial population based on rDNA analysis. RNA based analysis shows that Proteobacteria represented 28% of the clones sequenced. Similarly, RNA based microarray data showed Proteobacteria to be 8 times higher compared to DNA samples. Denaturing gradient gel electrophoresis (DGGE) targeting the b-Proteobacteria revealed no significant difference in diversity between the rDNA and rRNA samples. However, several bands were observed to be of much greater abundance for the rRNA sample. The results suggest that the Proteobacteria group may make a greater contribute to rumen metabolism than previously recognized but the functions of this group in the rumen require further investigation.