Topographic Map of Gammaproteobacteria using 16S rRNA gene sequence

Microbial identification is crucial for the study of infec- tious diseases. The classical method to attribute a specific name to a bacterial isolate to be identified is based on the comparison of morphologic and phenotypic characters to those described for type or typical strains. Recently a new naming approach based on bacteria genotype has been proposed and is currently under development. In this new approach phylogenetic relationships of bacteria could be determined by comparing a stable part of the genetic code. The part of the DNA commonly used for taxonomic purposes for bacteria is the 16S rRNA "housekeeping"gene. The 16S rRNA gene sequence analysis can be used to obtain a classification for rare or poorly described bacteria, to classify organisms with an unusual phenotype in a well defined taxon, to find misclassification that can lead to the discovery and description of new pathogens. The goal of this work is duo fold: the first one is to obtain a topographic representation of the bacteria clusters that allows to understand the relationships among them, the second one is to do that using genotype information without using a feature space. Many clustering works are conducted using a feature space where objects are represented. We did not use a vector space representation and we left the data in their original form