Short Unique Sequences in Bacterial Genomes as Strain- And Species-Specific Signatures

Abstract

The paper presents a new approach for phylotyping that can be potentially used for pure cultures and for mixed bacterial populations. It is based on the use of short unique nucleotide sequences (k-mers) that are present in the genomes of all strains of the same species and are absent in bacterial genomes of other taxonomic groups. We show that the number of such sequences depends on the percentage bias towards A/T or G/C base pairs, increasing for genomes with approximately equal composition. We found that the largest contribution to the set of primarily unique sequences is given by 16–17-mers, while sigmoidal curves reflecting the dependence of the number of unique sequences on the length of k-mers showed the maximum slope increment for k = 17, 18. Unique sequences of the length 16–18 bases can therefore be offered as potential markers. Comparing the sets of unique k-mers in the genomes of four Enterobacter strains, we estimated the level of their intraspecies stability and interspecies plasticity. As a result, we suggest discriminatory subsets as stencils for phylotyping, thereby increasing the list of genotyping markers with signatures of the new type.