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 N 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 N on the length of k-mers showed the maximum slope increment (ΔN/Δk) 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.
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