Until recently, I was not aware that bacteria can have more than two copies of ribosomal RNA (rRNA). I found a literature showing that a number of bacteria that have more than two copies of rRNA gene is considerably large (Acinas et al., 2004). For example,
Ureaplasma parvum has two copies of 16S rRNA gene that are slightly different in sequence [
link to ncbi], and, surprisingly,
Bacillus cereus has 13 copies, which are classified into 7 distinct sequences [
link to ncbi]! Therefore, classification of bacteria based only on 16S rRNA gene can overestimate the diversity of bacteria. Case et al. (2007) recommend to use
rpoB gene, a single-copy gene, in addition to the traditional 16S rRNA gene for genotyping bacteria in microbial ecological studies.
References
- Acinas SG, Marcelino LA, Klepac-Ceraj V & Polz MF (2004) Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons. Journal of Bacteriology 186: 2629-2635.
- Case RJ, Boucher Y, Dahllof I, Holmstrom C, Doolittle WF & Kjelleberg S (2007) Use of 16S rRNA and rpoB genes as molecular markers for microbial ecology studies. Applied and Environmental Microbiology 73: 278–288.
