Ribosomal RNA can be used to identify and compare bacteria based on evolutionary differences in the 16S ribosomal sequence region. The ribosomal RNA (rRNA) sequence contains genes encoding structural and functional portions of the ribosomes present in all bacteria and archaea and can be used to identify and distinguish different microbes. Highly conserved regions are used as primer binding sites to sequence the complete rRNA gene sequences. The hypervariable regions within the rRNA gene are used as species-specific signature sequences to identify the different microbes present in a sample.
16S and 18S small subunit (SSU)
23S and 28S large subunit (LSU)
SILVA sequence database
Ribosomal RNA sequence database for Bacteria, Archaea, and Eukarya
small (16S/18S SSU) and large subunit (23S/28S LSU) ribosomal RNA (rRNA) sequences
UNITE Community
fungal rDNA ITS sequences
https://unite.ut.ee/repository.php
Greengenes Database
Ribosomal Database Project
16S approaches have some limits in distinguishing different species, for example, Escherichia coli and Shigella spp. share almost identical 16S rRNA gene sequences. Ribosomal genes are expected to be highly conserved genes, remaining essentially unchanged throughout long periods of evolution. Also, it might be problematic that several organisms have multiple divergent rRNA operons and homologous recombination may occur between them (Gogarten et al. 2002)
Alternative approaches are developed to achieve higher resolution up to strain level by considered larger sets of genes
→ Multilocus sequence typing (MLST) 5-10 housekeeping genes (sub-species resolution)
Whole genome taxonomy
Sequencing the entire genome (shotgun sequencing) provides a higher taxonomic resolution than 16S.
→ MetaPhlAn - based on up to 200 species-specific marker-genes (sub-species resolution)
→ PanPhlAn - identify all genes of a strain present in a sample (strain-level resolution)