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

Toll-like receptor (TLR) signalling plays an important role in epithelial and immune cells of the intestine. TLR9 recognizes unmethylated CpG motifs in bacterial DNA, and TLR9 signalling 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 purine-purine-CG-pyrimidine-pyrimidine hexamers was linearly dependent on the genomic G+C content. We found that species belonging to Proteobacteria, Bacteroidetes and Actinobacteria (including bifidobacteria) carried high counts of GTCGTT, the optimal motif stimulating human TLR9. We also found that Enterococcus faecalis, Lactobacillus casei, Lactobacillus plantarum and Lactobacillus rhamnosus, whose strains have been marketed as probiotics, had 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 motif content of microbiota may depend on the host's physiological status and, consequently, on an adequate level of TLR9 signalling. We speculate that microbiota with increased numbers of microbes with CpG motif-rich DNA could better support mucosal functions in healthy individuals and improve the T-helper 1 (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, including CpG motifs, in gut microbiota could shed new light on host-microbe interactions across a range of diseases.