TABLE 5.
Similarity-based OTUs and richness estimates for general Bacteroidales swine source and environmental samples
| Sample source | No. of sequences | No. of OTUsa | Richness estimateb
|
Diversity index
|
|||
|---|---|---|---|---|---|---|---|
| Chao 1 (95% CIc) | ACE (95% CI) | Bootstrap | Shannon-Weaver (95% CI) | Simpson | |||
| Swine lagoon | 43 | 10 | 15 (11-42) | 19 (12-49) | 12 | 1.75 (1.52-1.97) | 0.17 |
| Swine manure pit | 209 | 59 | 122 (85-210) | 131 (92-215) | 74 | 3.18 (2.98-3.37) | 0.079 |
| Water adjacent to swine farms | 582 | 86 | 125 (103-173) | 138 (113-188) | 103 | 2.79 (2.63-2.95) | 0.19 |
| Swine feces | 199 | 55 | 86 (68-132) | 104 (77-164) | 68 | 2.84 (2.59-3.08) | 0.17 |
a
OTUs have been defined as each of the sequences that are at most 3% distant from the most similar sequence in a given OTU.
b
The Chao 1 estimator and abundance-based coverage estimator (ACE) are nonparametric methods used to estimate richness by adding a correction factor to the observed number of species (7, 8). Bootstrap is a nonparametric estimate of species richness as described by Smith and van Belle (33).
c
CI, confidence interval.