Table 2.
Comparison the two PCR methods in identifying the host species through DNA barcoding using fecal and cloacal samples
| Single PCR | Nested PCR | |||||
|---|---|---|---|---|---|---|
| Species | Order | No. tested | Successful PCR and Correct Species Identification | Mean Specimen Similarity ± Standard Deviation (%)e | Successful PCR and Correct Species Identification | Mean Specimen Similarity ± Standard Deviation (%) |
| FECAL SAMPLES | ||||||
| Anas clypeata | Anseriformes | 3 | 3 | 100±0 | 3 | 100.0±0.1 |
| Anas platyrhynchos | Anseriformes | 1 | 1 | 95.9±0 | 1 | 100±0 |
| Ardea cinerea | Ciconiiformes | 1 | 1 | 100±0 | 1 | 100±0 |
| Columba livia | Columbiformes | 2 | 1 | 100±0 | 2 | 100±0 |
| Gallus gallus | Galliformes | 29 | 18 | 97.9±4.4 | 29 | 99.9±0.3 |
| Numenius phaeopus | Charadriiformes | 1 | 1 | 100±0 | 1 | 100±0 |
| Phalacrocorax carbo | Pelecaniformes | 2 | 1 | 100±0 | 2 | 100±0 |
| Phasianus colchicus | Galliformes | 3 | 1 | 97.7±0 | 3 | 100±0 |
| Charadrius leschenaultii | Charadriiformes | 1 | 0 | 1 | 99.9±0 | |
| Platalea minor | Pelecaniformes | 3 | 0 | 3 | 99.7±0.1 | |
| Rostratula benghalensis | Charadriiformes | 1 | 0 | 1 | 99.9±0 | |
| Total | 47 | 27 | 47 | |||
| CLOACAL SAMPLES | ||||||
| Anas acuta | Anseriformes | 4 | 4 | 100±0 | 4 | 100±0.1 |
| Anas penelope | Anseriformes | 1 | 1 | 100±0 | 1 | 97.8±0.0 |
| Anas platyrhynchos | Anseriformes | 1 | 1 | 99.7±0 | 1 | 100±0 |
| Gallus gallus | Galliformes | 13 | 13 | 100±0 | 13 | 98.8±2.9 |
| Muscicapa dauurica | Passeriformes | 1 | 1 | 100±0 | 1 | 95.9±0 |
| Prinia gracilis | Passeriformes | 1 | 1 | 100±0 | 1 | 100±0 |
| Sturnus sericeus | Passeriformes | 8 | 8 | 99.9±0.3 | 8 | 99.9±0.1 |
| Tringa nebularia | Charadriiformes | 1 | 1 | 100±0 | 1 | 100±0 |
| Tringa totanus | Charadriiformes | 3 | 3 | 100±0 | 3 | 100±0 |
| Zosterops japonicus | Passeriformes | 1 | 1 | 100±0 | 1 | 100±0 |
| Acrocephalus orientalis | Passeriformes | 1 | 0 | 1 | 100±0 | |
| Halcyon smyrnensis | Coraciiformes | 1 | 0 | 1 | 94.9±0 | |
| Hirundo rustica | Passeriformes | 1 | 0 | 1 | 100±0 | |
| Luscinia cyane | Passeriformes | 1 | 0 | 1 | 99.9±0.0 | |
| Phalacrocorax carbo | Pelecaniformes | 1 | 0 | 1 | 100±0 | |
| Pycnonotus jocosus | Passeriformes | 1 | 0 | 1 | 99.9±0 | |
| Rostratula benghalensis | Charadriiformes | 5 | 0 | 5 | 99.9±0.0 | |
| Total | 45f | 34 | 45 | |||
e
Mean and standard deviation of specimen similarity in one species group: Similarity scores (specimen similarity) are calculated from the alignment of query sequence to that of known species in the barcoding database.
f
Four of the 45 cloacal samples did not yield a specific PCR product by the above methods. The DNA extracts from these 4 specimens, were re-extracted using the Qiagen Investigator Kit. Nested PCR was done for all 4 samples.