Table 2.
Differential abundance of OTUs in the different sample groups
| OTU | Taxon | Log2 (abundance ratio) | Adjusted p-value | |
|---|---|---|---|---|
| Pre-treatment/healthy | Post-treatment/healthy | |||
| Overabundant in subgingival plaque of subjects with chronic periodontitisa | ||||
| OTU_13 | Filifactor | 3.51 | 1.96 | 1.66E-09 |
| OTU_73 | Desulfobulbus | 3.45 | 1.93 | 6.29E-13 |
| OTU_75 | Eubacterium | 3.37 | 1.52 | 5.76E-16 |
| OTU_137 | Hallella | 3.34 | 1.06 | 1.44E-13 |
| OTU_4 | Porphyromonas | 3.16 | 1.33 | 6.57E-06 |
| OTU_63 | Phocaeicola | 3.10 | 1.22 | 8.52E-08 |
| OTU_12 | Tannerella | 3.10 | 1.53 | 6.79E-09 |
| OTU_111 | Unclassified (Bacteroidetes) | 3.07 | 1.26 | 6.69E-11 |
| OTU_55 | Alloprevotella | 3.05 | 3.46 | 1.62E-08 |
| OTU_8 | Porphyromonas | 3.02 | 2.17 | 9.20E-08 |
| OTU_25 | Unclassified (Firmicutes) | 2.96 | 1.39 | 2.12E-08 |
| OTU_58 | Unclassified (Firmicutes) | 2.93 | 2.20 | 2.11E-11 |
| OTU_66 | Unclassified (Firmicutes) | 2.92 | 1.33 | 2.18E-10 |
| OTU_110 | Johnsonella | 2.89 | 1.70 | 1.16E-11 |
| OTU_109 | Unclassified (Firmicutes) | 2.73 | 2.25 | 1.75E-15 |
| OTU_1773 | Treponema | 2.38 | 0.39 | 1.06E-06 |
| OTU_74 | Eubacterium | 2.35 | 0.86 | 2.08E-10 |
| OTU_129 | Treponema | 2.24 | 0.73 | 9.98E-06 |
| OTU_147 | Treponema | 2.23 | 2.00 | 1.47E-07 |
| OTU_606 | Treponema | 2.19 | 1.32 | 3.19E-06 |
| OTU_131 | Prevotella | 2.19 | 3.19 | 1.32E-08 |
| OTU_161 | Eubacterium | 2.15 | 0.14 | 1.74E-11 |
| OTU_62 | Mycoplasma | 2.14 | 0.75 | 3.24E-09 |
| OTU_72 | Leptotrichia | 2.14 | 2.19 | 2.67E-06 |
| OTU_101 | Treponema | 2.12 | 1.18 | 5.40E-09 |
| OTU_615 | Treponema | 2.11 | 0.86 | 1.18E-08 |
| OTU_97 | Mogibacterium | 2.06 | 0.90 | 4.84E-09 |
| OTU_33 | Treponema | 2.06 | 2.03 | 2.38E-05 |
| Overabundant in subgingival plaque of periodontally healthy subjectsa | ||||
| OTU | Taxon | Log2 (abundance ratio) | Adjusted p-value | |
| Healthy/pre-treatment | Healthy/post-treatment | |||
| OTU_98 | Exiguobacterium | 2.90 | 2.71 | 2.15E-16 |
| OTU_335 | Actinomyces | 2.73 | 4.33 | 1.12E-07 |
| OTU_7 | Veillonella | 2.52 | 2.31 | 2.86E-08 |
| OTU_159 | Paludibacter | 2.45 | 1.02 | 2.22E-16 |
| OTU_550 | Capnocytophaga | 2.44 | 1.38 | 5.77E-09 |
| OTU_15 | Actinomyces | 2.43 | 1.93 | 5.43E-09 |
| OTU_5 | Corynebacterium | 2.38 | 1.65 | 1.79E-06 |
| OTU_91 | Prevotella | 2.28 | 1.67 | 4.69E-07 |
| OTU_68 | Leptotrichia | 2.17 | 2.05 | 9.26E-07 |
| OTU_1327 | Veillonella | 2.15 | 2.02 | 1.98E-07 |
| OTU_1274 | Leptotrichia | 2.07 | 2.44 | 2.93E-07 |
| OTU_206 | Opitutus | 2.04 | 2.68 | 1.91E-15 |
| Overabundant in saliva of subjects with chronic periodontitisa | ||||
| OTU | Taxon | Log2 (abundance ratio) | Adjusted p-value | |
| Pre-treatment/healthy | Post-treatment/healthy | |||
| OTU_4 | Porphyromonas | 2.70 | 1.79 | 0.02179 |
| OTU_12 | Tannerella | 2.17 | 1.63 | 0.001173 |
| OTU_73 | Desulfobulbus | 2.13 | 1.20 | 0.000271 |
| OTU_74 | Eubacterium | 2.09 | 1.86 | 0.013454 |
| OTU_63 | Phocaeicola | 2.08 | 0.40 | 0.001862 |
| OTU_97 | Mogibacterium | 2.05 | 2.42 | 0.01061 |
| Overabundant in Saliva of Periodontally Healthy Subjectsa | ||||
| OTU | Taxon | Log2 (abundance ratio) | Adjusted p-value | |
| Healthy/pre-treatment | Healthy/post-treatment | |||
| OTU_57 | Prevotella | 2.33 | 2.35 | 0.00377 |
a Analysis was conducted in metagenomeSeq after removing OTUs that contained <15 total occurrences across all samples (i.e., low-abundance taxa). The linear model used for the zero-inflated Gaussian ZIG) fit was ~Treatment + normFactor. This table shows only those OTUs with >50% effective sample size and adjusted p-values < 0.05. The coefficients for overabundant taxa in healthy vs. diseased samples are negative in the linear model fit