Phylogenomics cover the field of phylogenetic reconstruction on the genome scale. This promises a better resolution and more reliable phylogenies than single-gene or multi-locus sequence analyses but usually requires elaborated bioinformatics infrastructures necessary to handle and explore large amounts of both genome and physiological data (Meier-Kolthoff et al. 2013c,e).Knowledge of the phenotypic, genotypic and biological characteristics of a microorganism is imperative in differentiating it from its pathogenic and/or toxigenic relatives or other microorganisms that are detrimental to the health of plants, animals, humans and the environment.
Microbial taxonomy is the rank-based classification of bacterial and archaeal strains and takes into account all available phenotypic as well as genotypic data and integrates them in a consensus type of classification (polyphasic taxonomy). Today, genome- and proteome-scale data are the basis for novel bioinformatics techniques for the classification and identification of microorganisms that can replace conventional methods entirely due to advantages such as accuracy, speed and reproducibility (Meier-Kolthoff et al. 2013a,b; Meier-Kolthoff et al. 2014a).