Table 2.
Mean estimates of alpha diversity metrics (mean ± S.D., p-values) calculated for each method from OTU tables rarefied to 11,739 sequences per sample.
| Method | Chao1 | Observed OTUs | Shannon diversity | Simpson diversity |
|---|---|---|---|---|
| HMP | 842 ± 64.9 (p = 1.0) | 533 ± 44.8 (p = 0.32) | 5.28 ± 0.41 (p = 0.01) | 0.90 ± 0.04 (p = 0.02) |
| M | 818 ± 90.1 (p = 0.33) | 528 ± 46.0 (p = 0.04) | 5.18 ± 0.64 (p = 0.01) | 0.87 ± 0.09 (p = 0.02) |
| P | 825 ± 61.4 (p = 0.24) | 524 ± 38.4 (p = 0.02) | 5.19 ± 0.52 (p = 0.01) | 0.89 ± 0.07 (p = 0.01) |
| Q | 825 ± 87.3 (p = 0.52) | 531 ± 48.8 (p = 0.16) | 5.13 ± 0.69 (p = 0.01) | 0.87 ± 0.09 (p = 0.01) |
| Z | 865 ± 61.0 | 562 ± 42.6 | 5.94 ± 0.30 | 0.94 ± 0.03 |
Each method represents data from 27 samples. P-values reported in the table are only associated with pairwise comparisons with Z method. No other pairwise comparisons between methods resulted in significant p-values (p < 0.05).