Table 3.
A summary of 18S and 28S rDNA primer set evaluation.
| EMP (1391F/EukBr) | 563F/1132R | 616*F/1132R | 1183F/1631R | DM568F/RM2R | RM2F/RM3R | GA12F/RM4R | GA20F/RM9R | |
|---|---|---|---|---|---|---|---|---|
| rDNA | 18S | 18S | 18S | 18S | 28S | 28S | 28S | 28S |
| Target variable region | V9 | V4–5 | V4–5 | V7–8 | D4–5 | D4–5 | D4–6 | D8–9 |
| Degeneracy (forward/reverse) | 0/0 | 3/3 | 4/3 | 0/0 | 0/1 | 1/1 | 0/5 | 1/1 |
| Amplicon size (bp)a | 145 | 569 | 516 | 449 | 284 | 236 | 507 | 505 |
| Bacterial contamination | − | −− | + | ++ | ++ | ++ | ++ | ++ |
| Taxonomic coverage b | ||||||||
| Nematoda | + | ++ | ++ | ++ | + | ++ | ++ | ++ |
| Platyhelminthes | + | ++ | ++ | ++ | + | ++ | ++ | ++ |
| Acanthocephala | + | ++ | ++ | − | ++ | ++ | ++ | ++ |
| Coccidia | + | ++ | ++ | ++ | ++ | ++ | ++ | ++ |
| Cryptosporida | + | ++ | ++ | ++ | ++ | ++ | ++ | ++ |
| Haemosporidia | + | − | − | − | ++ | ++ | − | ++ |
| Fornicata | + | ++ | + | + | + | − | − | ++ |
| Discicristata | + | ++ | + | ++ | + | + | ++ | + |
| Parabasalia | + | ++ | + | − | ++ | − | + | ++ |
| Entamoebida | + | ++ | ++ | − | ++ | − | − | − |
| Longamoebia | + | ++ | ++ | ++ | ++ | ++ | ++ | ++ |
aBased on S. cerevisiae rRNA gene (NC_001144).
b++; >85%, +; 10–85%, −; <10% in the in silico taxonomy coverage test. Bold characters indicate detections confirmed using MiSeq sequencing in this study.