SSCP Analysis of V3 Region of 16S rRNA for the Characterization of Rumen Microbiome of Goat

Molecular ecology techniques based on small subunit (SSU) rRNA sequences can potentially provide a complete description of the rumen microbes. The present study describes the PCRSSCP analysis of V3 region of 16S rRNA as a potential target to characterize the rumen microbiome using metagenomic DNA. All the hundred DNA samples isolated from the goat rumen liquor were subjected to amplification of 16S rRNA gene using a Bacterial universal primer. The V3 region of 16S rRNA was amplified using first round PCR product as template. Sixty-three samples showed positive for amplification of V3 region. Those PCR products were screened for SSCP and found eleven different SSCP patterns. Five representative samples which had produced five different SSCP pattern were sequenced and subjected to sequence analysis. The sequence analysis of V3 region and phylogenetic tree indicated that the DNA sequence of V3 region was found to cluster differently and found to be in association with the SSCP profile of V3 region. Thus the V3 region of 16S rRNA truly reflected the rumen bacterial community. Therefore, it is recommended that the PCR-SSCP of V3 region as an alternative to study the bacterial diversity and its identification in the rumen in place of costintensive metagenomic approaches.