Table 1.
Summary of patients and category.
Figure 1.
Shannon diversity index of genus- (A) and species-level (B) OTUs in the deep and shallow sites.
*, p-value<0.05; **, p-value<0.01.
Figure 2.
Genus-level OTUs with >1.0% of abundance in at least one patient in deep and/or shallow sites.
Colors reflect the abundance of OTUs from high (red) to low (black); gray, OTU missing.
Figure 3.
Genus-level OTUs significantly different between shallow and deep pockets.
Of 170 genera, 51 showed a statistically significant difference in abundance (%) between shallow and deep sites. Data were statistically analyzed by the two-part model and false discovery rate (FDR). The FDR q-value of 51 genera was <0.05 which represents significant difference between shallow and deep samples. Inserted figure, phylum-level OTUs significantly different between shallow and deep sites; **, p-value <0.01; ***, p-value <0.001.
Figure 4.
Clustering analysis of log2 ratio of deep abundance to the shallow at genus level using Hierarchical Trees (HCL).
The data were obtained using log2 ratio (deep abundance/shallow abundance). Both deep and shallow abundance had 0.00001 added due to the many zeros in the samples. The genera present in fewer than 10% of samples were excluded. The genera were clustered into two groups (I and II) and 88 patients were grouped into two types (A and B), each of which contains 2 subtypes (A1 and A2, B1 and B2).
Table 2.
Associations of patient types with other factors
Figure 5.
The species associated with dental caries.
The abundances of species-level OTUs were statistically analyzed in 3 levels of dental caries in deep and shallow sites, respectively. The species with a significant difference (α = 0.05) in 3 levels of dental caries were shown. HD_shallow, high decay and shallow site; MD_shallow, moderate decay and shallow site; ND_shallow, non-decay and shallow site; HD_deep, high decay and deep site; MD_ deep, moderate decay and deep site; ND_ deep, non-decay in deep site.
Table 3.
Association of species-level microbiome with dental caries in deep and shallow sites.