Immunostimulatory CpG motifs in the genomes of gut bacteria and their role in human health and disease

Toll-like receptor (TLR) signaling plays an important role in epithelial and immune cells of the intestine. TLR9 recognizes unmethylated CpG motifs in bacterial DNA and TLR9 signaling maintains the gut epithelial homeostasis. Here, we carried out a bioinformatic analysis of the frequency of CpG motifs in the genomes of gut commensal bacteria across major bacterial phyla. The frequency of potentially immunostimulatory CpG motifs (all CpG hexamers) or PuPuCGPyPy hexamers was linearly dependent on the genomic GC content. We found that species belonging to Proteobacteria, Bacteroidetes and Actinobacteria (including bifidobacteria) carry high counts of GTCGTT, the optimal motif stimulating human TLR9. We also found that Enterococcus faecalis, Lactobacillus casei, L. plantarum and L. rhamnosus, whose strains have been marketed as probiotics, have high counts of GTCGTT motifs. As gut bacterial species differ significantly in their genomic content of CpG motifs, the overall load of CpG motifs in the intestine depends on the species assembly of microbiota and their cell numbers. The optimal CpG composition of microbiota may depend on the host's physiological status and, consequently, on the adequate level of TLR9 signaling. We speculate that microbiota with increased numbers of microbes with CpG motif-rich DNA could better support the mucosal functions in healthy individuals and improve the Th1/Th2 imbalance in allergic diseases. In autoimmune disorders, CpG motif rich DNA could, however, further increase the Th1 type immune responsiveness. Estimation of the load of microbe associated molecular patterns (MAMPs), including CpG motifs, in the gut microbiota could shed new light into host-microbe interactions across a range of diseases