16S rDNA Analysis of Bacterial Diversity in Three Fractions of Cow Rumen

The bacterial diversity of the bovine rumen was examined using a PCR-based approach. 16S rDNA sequences were amplified and cloned from three fractions of rumen (solid, fluid, and epithelium) that are likely to represent different bacterial niches. A total of 113 clones were sequenced, and similarities to known l6S rDNA sequences were examined. About of the sequences had similarity to 16S rDNA database sequences. Furthermore, about of the sequences were similar to 16S rDNA database sequences. For the remaining , the similarity was less than . Phylogenetic analysis was also used to infer the makeup of the bacterial communities in the different rumen fractions. The Cytophaga-Flexibacter-Bacteroides group (CFB, ), low G+C Gram-positive bacteria (LGCGPB, ), and Proteobacteria were represented in the rumen fluid clone set; LGCGPB , CFB, Proteobacteria , high G+C Gram-positive bacteria (HGCGPB, ), and Spirochaetes were represented in the rumen solid clone set; and the CFB group and LGCGPB were represented in the rumen epithelium clone set. These findings suggest that the rumen fluid, solid, and epithelium support different microbial populations that may play specific roles in rumen function.