Topographic maps for clustering and fast identification of bacteria using 16s housekeeping gene

In microbial identification the standard method to attribute a specific name to a bacterial isolate relays on the comparison of morphologic and phenotypic characters to those described for type or typical strains. In the last years a new standard for identifying bacteria using genotypic information began to be developed. In this new approach phylogenetic relationships of bacteria could be determined by comparing a stable part of the bacteria genetic code, the so called “housekeeping genes”. The most commonly used gene for taxonomic purposes for bacteria is the 16S rRNA. The goal of this chapter is to show that genotypic features can be used to build a topographic map for clustering of a large set of bacteria. The map allows to visually inspect the relative distances among sequences of different orders or classes. Moreover it can be used for fast identification of suspect sequences of bacteria, using a small set of sequences prototypes.