16S rDNA analysis of bacterial diversity in three fractions of cow rumen

Abstract

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 16S 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.