16S rDNA Analysis 9f 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 $47.8\%$ of the sequences had $90-97\%$ similarity to 16S rDNA database sequences. Furthermore, about $62.2\%$ of the sequences were $98-100\%$ similar to 16S rDNA database sequences. For the remaining $6.1\%$, the similarity was less than $90\%$. Phylogenetic analysis was also used to infer the makeup of the bacterial communities in the different rumen fractions. The Cytophaga-Flexibacter-Bacteroides group (CFB, $67.5\%$), low G+C Gram-positive bacteria (LGCGPB, $30\%$), and Proteobacteria $(2.5\%)$ were represented in the rumen fluid clone set; LGCGPB $(75.7\%)$, CFB$(10.8\%)$, Proteobacteria $(5.4\%)$, high G+C Gram-positive bacteria (HGCGPB, $5.4\%$), and Spirochaetes $(2.7\%)$ were represented in the rumen solid clone set; and the CFB group $(94.4\%)$ and LGCGPB $(5.6\%)$ 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.