16s rDNA analysis of the bacterial diversity in the rumen of the Philippine carabao (Bubalis bubalis L.)
2009
Nguyen, M.H.R.
The total community DNA from rumen digesta of two fistulated carabaos was obtained and 16s rDNA clonal libraries were constructed. Plasmids were isolated from 160 clones and 27 plasmids were sequenced. Thirteen sequences were found to be suitable for use in phylogenetic analysis. They were compared to reference sequences in the GeneBank database using the BLAST search tool found in the NCBI website. A phylogenetic tree was constructed using Clustal X 2.0.11 and viewed using TreeView 1.6.6. A clone was identified to be 97% similar to Succiniclasticum ruminis. Another clone showed a 96% similarity with S. ruminis. The other 11 clones showed similarities with identified rumen bacterial clones (92%-99%). Most of the 16s rDNA genes (61.5%, 8 out of 13) are most similar to and can be classified under the low G+C phylum, three of the 13(23.1%) 16s rDNA sequences are grouped under the proteobacteria, one sequence (7.7%) is probably a 16s rDNA gene of a bacterium that belongs to the Cytophaga-Flexibacter-Bacteroides subphylum, and one sequence (7.7%) remains unclassified.
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