Table 3. Estimators of sequence library diversity, evenness and coverage.
Estimators were calculated using EstimateS, for each of the 11 clone libraries described in this study, as well as for the combined sequence set. 1–10, individual pools; S, subgingival pool. Evenness was calculated using the formula (EXP(Shannon))/Sobs, in which Sobs is the observed number of species (OTUs). Good’s estimator of coverage was calculated using the formula: (1-(singletons/individuals))*100.
| 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | S | Combined | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Number of clones | 1048 | 1032 | 1070 | 1019 | 1055 | 931 | 999 | 1039 | 1036 | 1056 | 1083 | 11368 |
| Number of OTUs | 111 | 75 | 107 | 126 | 97 | 73 | 68 | 65 | 117 | 67 | 128 | 247 |
| Number of Singletons | 28 | 17 | 25 | 49 | 24 | 22 | 26 | 24 | 35 | 13 | 47 | 39 |
| Number of Doubletons | 13 | 9 | 15 | 15 | 18 | 8 | 9 | 7 | 20 | 9 | 20 | 20 |
| Chao 1 (richness) | 138.0 | 88.6 | 125.8 | 199.5 | 111.5 | 98.7 | 100.5 | 99.5 | 145.3 | 74.8 | 179.5 | 282.3 |
| Shannon (Diversity) | 3.82 | 3.31 | 3.9 | 3.88 | 3.61 | 3.03 | 2.7 | 2.76 | 3.75 | 3.01 | 3.88 | 4.03 |
| Simpson (Diversity) | 26.13 | 15.81 | 30.51 | 28.92 | 21.94 | 9.31 | 8.20 | 7.12 | 16.95 | 10.27 | 27.35 | 26.24 |
| Evenness | 0.41 | 0.37 | 0.46 | 0.38 | 0.38 | 0.28 | 0.22 | 0.24 | 0.36 | 0.30 | 0.38 | 0.23 |
| Goods estimator of coverage | 97.33 | 98.35 | 97.66 | 95.19 | 97.73 | 97.63 | 97.40 | 97.69 | 96.62 | 98.77 | 95.66 | 99.66 |