PCR and qPCR-based applications in rumen microbiology research: a review

The rumen and its microbial ecosystem play a central role in the overall nutrition and health of ruminant animals. However, development and homeostatic state of the entire gut system is influenced by different interrelated factors. Recent developments in molecular diagnostic tools by using amplicon sequencing of 16S ribosomal RNA and use of high-throughput data generated through applications of pyrosequencing is a promising approach to defining the rumen microbial genome. Several procedures such as genome-wide shotgun sequencing for metagenomic data generation to predict how the rumen microbiota works, bacterial DNA integration in order to construct or edit genomes of isolated microbes and several other “omic”-based technologies based on PCR and real-time PCR (qPCR), have elucidated the complexity of the rumen microbiota. These tools are more sensitive and precise in quantitation, identification and functional characterisation of the entire rumen microbiome. PCR/qPCR enables investigations of changes in the microbiome and microbiota with respect to age, diet, species and environmental variations thus providing new information about rumen microbial genome. In this review, we will highlight recent findings using PCR and qPCR-based procedures in investigating the complex nature of the rumen microbial population which has advanced our knowledge and understanding of the rumen microbiome.