Genetic markers for rumen microbial diversity
16S and 18S rRNA gene The 16S ribosomal RNA (rRNA)
gene (∼1,550 bp) exists universally in bacteria, contains
both variable and conserved regions, and is regarded as a
gold standard in microbial ecology studies (Woese et al.
1976; Woese 1987; Case et al. 2007; Lozupone and
Knight 2008; Lemos et al. 2011). This gene can be compared
not only among all bacteria but also with the 16S
rRNA gene of archaea and the 18S rRNA gene of eukaryotes
(Clarridge III 2004). This gene has sufficient interspecific
polymorphisms to provide distinguishing and
statistically valid measurements for phylogenetic analysis;
therefore, it has found large applications in bacterial reclassification
and identification of a number of uncultured species
(Case et al. 2007; Rajendhran and Gunasekaran 2011).
The analysis of amplified and/or sequenced 16S/18S rRNA
genes has become the most important approach for rumen
microbial studies (Tables 2, 3, and 4).