Comparative genome analysis and identification of competitive and cooperative interactions in a polymicrobial disease

Abstract

Polymicrobial diseases are caused by combinations of multiple bacteria, which can lead to not only mild but also life-threatening illnesses. Periodontitis represents a polymicrobial disease; Porphyromonas gingivalis, Treponema denticola and Tannerella forsythia, called 'the red complex', have been recognized as the causative agents of periodontitis. Although molecular interactions among the three species could be responsible for progression of periodontitis, the relevant genetic mechanisms are unknown. In this study, we uncovered novel interactions in comparative genome analysis among the red complex species. Clustered regularly interspaced short palindromic repeats (CRISPRs) of T. forsythia might attack the restriction modification system of P. gingivalis, and possibly work as a defense system against DNA invasion from P. gingivalis. On the other hand, gene deficiencies were mutually compensated in metabolic pathways when the genes of all the three species were taken into account, suggesting that there are cooperative relationships among the three species. This notion was supported by the observation that each of the three species had its own virulence factors, which might facilitate persistence and manifestations of virulence of the three species. Here, we propose new mechanisms of bacterial symbiosis in periodontitis; these mechanisms consist of competitive and cooperative interactions. Our results might shed light on the pathogenesis of periodontitis and of other polymicrobial diseases.

Figure 1

Dotplot analysis of T. forsythia, T. denticola and P. gingivalis. A dot is plotted when the 20-bp sequences exhibited similarity between two genomes. The dots are colored according to the similarity score, with gradation from 70% (blue) to 100% (red).

Figure 2

The dN/dS ratio of T. forsythia, T. denticola and P. gingivalis. The dN/dS ratios of all the gene clusters in this analysis are shown in an ascending order for (b) 19 T. forsythia, (b) 14 T. denticola and (c) 5 P. gingivalis strains, respectively. Red squares indicate the genes that correspond to the condition dN/dN>1.

Figure 3

Similarity searches of CRISPR spacers in T. forsythia. In the T. forsythia CRISPR spacers, the presence of the targets is shown as a pie chart, where the targets of the 106 spacers are shown as other charts. The targets of the 25 spacers against the bacteria other than the three red complex species are indicated by the species names.

Figure 4

Metabolic analyses of T. forsythia, T. denticola and P. gingivalis. (a) The stand-alone pathways in the small pathway groups are colored if they are mapped by the core genes of either one, two or three species, as follows: gray (a known metabolic pathway), green (T. forsythia), blue (T. denticola), red (P. gingivalis), purple (T. forsythia and T. denticola), yellow (T. denticola and P. gingivalis), pink (P. gingivalis and T. forsythia), light blue (T. forsythia, T. denticola and P. gingivalis), respectively. (b) A fatty acid synthesis pathway group, which includes a butyric acid pathway, is shown by enlarging the corresponding region in (a). (c) In the butyric acid pathway, the gene required for each change of substance is shown, with the colors described in (a).