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Background  In streptococci of the mitis group, competence for natural transformation is a transient physiological state triggered by competence stimulating peptides (CSPs). Although low transformation yields and the absence of a widespread functional competence system have been reported for  Streptococcus mitis , recent studies revealed that, at least for some strains, high efficiencies can be achieved following optimization protocols. To gain a deeper insight into competence in this species, we used RNA-seq, to map the global CSP response of two  transformable strains : the type strain NCTC12261 T  and SK321.    Results  All known genes induced by ComE in  Streptococcus pneumoniae , including  sigX , were upregulated in the two strains. Likewise, all sets of streptococcal SigX core genes involved in extracellular DNA uptake, recombination, and fratricide were upregulated. No significant differences in the set of induced genes were observed when the type strain was grown in rich or semi-defined media. Five upregulated operons unique to  S. mitis  with a SigX-box in the promoter region were identified, including two specific to SK321, and one specific to NCTC12261 T . Two of the strain-specific operons coded for different bacteriocins. Deletion of the unique  S. mitis sigX  regulated genes had no effect on transformation.    Conclusions  Overall, comparison of the global transcriptome in response to CSP shows the conservation of the ComE and SigX-core regulons in competent  S. mitis  isolates, as well as species and strain-specific genes. Although some  S. mitis  exhibit truncations in key competence genes, this study shows that in transformable strains, competence seems to depend on the same core genes previously identified in  S. pneumoniae .    Electronic supplementary material  The online version of this article (10.1186/s12864-018-4802-y) contains supplementary material, which is available to authorized users.

High-resolution profiles of the Streptococcus mitis CSP signaling pathway reveal core and strain-specific regulated genes