Sequence-Based Classification and Identification of Prokaryotes

Abstract

Bioinformatics is important to classification and identification since all prokaryotes have been classified based on the phylogeny of the 16S rRNA gene sequence and this character has also to a great extent been the gold standard for identification as well. Whole genomic sequences are increasingly used for classification and identification. This includes in silico estimates of DNA-DNA hybridization which has been used for the classification of all species. Classifications of species, genera, families, orders, classes, and phyla are achieved by 16S rRNA sequence-based phylogenetic analysis and more recently phylogenetic analysis of other conserved genes and proteins mainly determined by whole genomic sequencing. The rules for the naming of prokaryotes have been formulated in the International Code of Nomenclature of Prokaryotes. Sequence-based identification can be complemented by other genes besides the 16S rRNA gene sequences. The rpoB gene sequence is frequently used since it allows the separation of some species that cannot be identified by 16S rRNA gene sequence comparison. Identification of prokaryotes that cannot be cultured is possible by 16S rRNA gene amplicon sequencing as further described in Chap. 8.