Delineating bacterial subspecies Additional file 3 to : “ Complete genome sequence of DSM 30083 T , the type strain ( U 5 / 41 T ) of Escherichia coli , and a proposal for delineating subspecies in microbial taxonomy

We here describe our approach to finding clustering parameters suitable for delineating subspecific bacterial lineages using the same intergenomic distances that can be used to estimate digital DNA:DNA hybridization values (Meier-Kolthoff et al. 2013, 2014). A main issue to be taken into account here is that clustering algorithms such as single or complete linkage clustering make no use of types such as type strains (in bacterial taxonomy) or type specimens (in zoology or botany). In contrast, taxonomic assessments such as the establishment of a new species can ultimately only be assessed by comparing with types. For instance, the 70% (d)DDH rule makes only sense if applied to the comparison of two type strains or of one non-type strain with a type strain (Meier-Kolthoff et al. 2014).