Molecular Characterization and Diversity of Rumen Bacterial Flora in Indian Goat by 16S rDNA Sequencing

Abstract

Present study was aimed to characterize bacterial communities in goat rumen using a culture-independent approach for a pooled sample of rumen fluid from five adult surti goats. Due to their unique browsing habits including feeding on unconventional tree leaves, goats are expected to host distinct bacterial communities in their rumen. So, 16S rDNA sequences were amplified and cloned from the sample and 60 such clones were sequenced to evaluate the bacterial diversity in goat rumen. Sequence similarity search with Genbank databases revealed that five clones (8%) exhibited similarities with known bacterial species (viz. Ruminococcus albus, Ruminococcus flavefaciens, Prevotella multiformis {2 clones} and Butyrivibrio fibrisolvens) and five clones (8%) showed similarities with known bacterial genera (viz., Ruminococcus, Prevotella, and Bacillus {3 clones}). Taxonomic classification by Ribosomal Database Project (RDP) revealed that the 60 clones mainly belonged to two phyla viz. Bacteriodes (21 clones) and Firmicutes (20 clones), however, 17 clones fell under unclassified bacteria and two clones under unclassified root. Phylogenetic analysis using neighbour-joining method grouped three clones (5%) with species, two clones (3%) with genera, one clone (1.6%) with family, twenty seven clones (45%) with unidentified rumen bacteria and the remaining twenty seven clones (45%) grouped separately and showed distinct genetic grouping compared to the reported sequences in the Genbank database.