TABLE 2.
Sequence diversity, coverage, and taxonomic complexity by groups of patients
| Measurement |
H. pylori statusa |
Proton pump inhibitor status |
|||
|---|---|---|---|---|---|
| Positive (n = 9) | Negative (n = 15) | Treated (n = 12) | Untreated (n = 12) | Combined (n = 24) | |
| No. of sequences | |||||
| Total | 95,949 | 95,709 | 103,912 | 87,746 | 191,658 |
| Assigned | 95,758 | 93,854 | 103,519 | 86,093 | 189,612 |
| Unassigned | 191 | 1,855 | 393 | 1,653 | 2,046 |
| Helicobacter sequences | 45,739 | 994 | 15,834 | 30,899 | 46,733 |
| No. of OTUsb | 304 | 479 | 419 | 378 | 519 |
| Chao1 estimator of species richness | 313.9 | 479.6 | 423.0 | 387.5 | 519.0 |
| Shannon's index for diversity | 3.5 | 5.7 | 4.9 | 4.6 | 4.9 |
| Simpson's index for diversity | 0.7 | 0.9 | 0.9 | 0.8 | 0.9 |
| Evennessc | 0.4 | 0.6 | 0.6 | 0.5 | 0.5 |
| Good's estimator of coverage (%) | 99.9 | 99.9 | 99.9 | 99.9 | 100 |
| Classification success (% [no. of identified taxa]) | |||||
| Phylum | 70.6 (12) | 100 (17) | 94.1 (16) | 88.2 (15) | 100 (17) |
| Family | 77.1 (64) | 94.0 (78) | 85.5 (71) | 91.6 (76) | 100 (83) |
| Genus | 64.3 (74) | 94.8 (109) | 81.7 (94) | 82.6 (95) | 100 (115) |
a
As determined by conventional testing.
b
OTU, operational taxonomic unit.
c
The Shannon's index of evenness was calculated using the formula E = eD/N, where D is the Shannon diversity index.