Table 2.
Summary of the 454 pyrosequencing data.
| Sample | # of raw seqs assigned | # of sequences after screening | # of preclustered seqs after screening | Observed OTUs | Maximum # of OTUs | Good's coverage∗∗ | |||
|---|---|---|---|---|---|---|---|---|---|
| Mothur | USEARCH | Rarefaction asymptote∗ | Chao1 | ACE | |||||
| CD-1 | 98021 | 91456 | 21080 | 3973 | 8899 | 6001 | 10657 | 19318 | 95.7% |
| CD-2 | 98238 | 91227 | 12437 | 2829 | 5162 | 4278 | 7806 | 14361 | 96.9% |
| CM-1 | 5457 | 2714 | 598 | 135 | 324 | 259 | 370 | 1121 | 95.0% |
| CM-2 | 5273 | 2506 | 330 | 114 | 199 | 205 | 287 | 580 | 95.5% |
| TD-1 | 56959 | 53527 | 10304 | 1891 | 4252 | 2779 | 5114 | 9286 | 96.5% |
| TD-2 | 57442 | 49836 | 6685 | 1484 | 2706 | 2188 | 3971 | 6948 | 97.0% |
| TM-1 | 8104 | 30 | 23 | 17 | 19 | 63 | 63 | 246 | 43.3% |
| TM-2 | 8683 | 33 | 19 | 15 | 16 | 19 | 18 | 21 | 54.5% |
CD, chicken cecal digesta; CM, chicken ileal mucosa; TD, turkey cecal digesta; TM, turkey ileal mucosa.
∗Estimated by Number of phylotypes = α(1 − β × e[−κ × n]).
∗∗Estimated by Coverage of diversity = (n − N)/n × 100%.