Role of immunostimulatory deoxycytidylate-phosphate-deoxyguanylate (CpG) motifs in oral bacteria associated with oral diseases

Abstract

Background: CpG oligodeoxynucleotide motifs in bacterial DNA with composition variations exhibit potent immunostimulation. The effect of different compositions in oral infections is unclear. This study aims to investigate CpG motifs in bacteria associated with endodontic diseases, periodontal diseases, and dental caries to elucidate their influence on host immune response.

Methods: Fifty oral bacterial genomes were selected for in silico analysis to determine GC% content and CpG motif frequency in each genome. The relationships between GC% content, CpG motif frequency, and genome size were assessed using correlation analysis. Normalisation of immunostimulatory sequences was implemented to enable unbiased comparison of frequency counts among bacteria.

Results: Sixty percent of bacteria exhibited medium GC% content (Mdn = 44), with no significant difference among bacteria associated with these diseases (p = 0.66). A positive correlation between GC% content and CpG motif frequency, as well as genome size and CpG motifs frequency was observed. A higher-than-mean of the human immunostimulatory motif (GTCGTT, 7/14) and the mice/rabbits immunostimulatory motif (GACGTT, 9/14) was observed in core endodontic microbiota.

Conclusion: CpG motifs in oral bacteria might drive disease progression through host immunomodulation. Variation in bacterial CpG motifs suggests targeting these motifs offers a promising therapeutic intervention.

Keywords: CpG; caries; endodontic diseases; genome; immunostimulatory; oral bacteria; periodontal diseases.

Figure 1.

A comparison of GC% content of bacteria across four disease groups: dental caries, endodontic diseases, periodontal diseases, and multiple oral diseases. (a) Most bacteria in our study (60%) exhibit medium GC% content. Bacteria associated with dental caries present medium to high GC% content, whereas bacteria in the remaining groups show low to medium GC% content. (b) The median GC% content of bacteria in each group was 46.5 for dental caries, 40 for endodontic disease, 44.5 for periodontal disease, and 43.5 for multiple oral diseases. No significant difference in GC% content was observed among the groups, p = 0.66.

Figure 2.

The correlation between CpG frequency with GC% content and genome size are shown. (a) The frequency of CpG motifs increased with rising GC% content (r = 0.94). (b) CpG motifs frequency also positively correlated with the genome size (r  = 0.74). (c) The frequency of MRIM (GACGTT) increased with rising GC% content (r = 0.77). (d) A positive correlation was also observed with MRIM (GACGTT) frequency and genome size (r = 0.81). (e) The frequency of HIM (GTCGTT) increased with rising GC% content. (f) The frequency of HIM (GTCGTT) also positively correlated with genome size (r = 0.75).

Figure 3.

Following normalisation, the frequencies of MRIM (GACGTT) and HIM (GTCGTT), were illustrated. (a) The mean frequency of MRIM (GACGTT) was 7, with 25 bacteria exceeding this mean, 5 had the mean frequency, and 20 bacteria were below the mean. (b) HIM (GTCGTT) mean frequency was found to be 9, with 22 bacteria exhibiting frequency above the mean, 9 possessing the mean frequency, and 19 falling below. Black represents cariogenic bacteria, red represents endodontic bacteria, green represents periodontal bacteria, and blue represents bacteria related to multiple oral diseases.