Table 2.
In silico taxonomic coverage of host-associated helminths/protozoa and fungi for published and newly designed 18S V4 primer sets
| n = 3097 | n = 2913 | Rank | Rank sum | n = 9373 | |||
|---|---|---|---|---|---|---|---|
| Primer ID | Mean | Helminths | Protozoa | Helminths | Protozoa | Fungi | |
| Owens 29F | 96.8% | 95.5% | 98.0% | 1 | 1 | 2 | 91.1% |
| Owens 2-2b | 96.4% | 94.9% | 97.9% | 2 | 2 | 4 | 92.2% |
| Owens 13F | 96.4% | 94.9% | 97.9% | 2 | 2 | 4 | 92.4% |
| Owens 9F | 95.2% | 94.4% | 96.0% | 4 | 4 | 8 | 92.4% |
| Bates | 88.2% | 80.4% | 95.9% | 8 | 5 | 13 | 93.7% |
| Hugerth | 84.5% | 93.1% | 75.8% | 5 | 8 | 13 | 94.1% |
| Krogsgaarda | 81.0% | 93.0% | 69.0% | 6 | 9 | 15 | 91.8% |
| Hadziavdic 566 | 78.7% | 76.4% | 81.0% | 10 | 6 | 16 | 91.4% |
| DeMonea | 75.3% | 86.4% | 64.1% | 7 | 11 | 18 | 81.8% |
| Stoeck | 63.8% | 49.1% | 78.4% | 13 | 7 | 20 | 79.4% |
| Machida | 61.7% | 78.1% | 45.2% | 9 | 14 | 23 | 92.5% |
| Bradley | 58.0% | 48.9% | 67.1% | 14 | 10 | 24 | 69.5% |
| Hadziavdic 574 | 55.6% | 48.3% | 62.9% | 15 | 12 | 27 | 78.9% |
| Comeau | 54.9% | 65.3% | 44.5% | 11 | 15 | 26 | 91.4% |
| C-S/Geisenb | 47.5% | 40.7% | 54.2% | 16 | 13 | 29 | 93.0% |
| C-S/Brate 2b | 36.8% | 50.8% | 22.8% | 12 | 17 | 29 | 90.0% |
| Woodb | 28.7% | 32.2% | 25.2% | 17 | 16 | 33 | 45.1% |
| Zhanb | 14.0% | 5.7% | 22.3% | 19 | 18 | 37 | 83.6% |
| C-S/Brate 1b | 13.5% | 5.8% | 21.1% | 18 | 19 | 37 | 93.8% |
Bold font indicates overall metrics (mean and rank sum). See Supplementary Table 1 for full primer names and sequences.
The first four rows represent primers designed in this study.
%, % coverage calculated allowing for 1 mismatch with a 2-base pair 3′ window using the SILVA 138 SSU rRNA NR Ref database; n, number of eligible accessions; Mean, mean coverage of all parasite/commensal groups.
aMultiple primer sets combined for analysis.
b<50% overall mean target complementarity.