Table 1.
List of primer sets targeting the 18S rRNA gene and their coverage in 14 taxonomic groups.
| Taxonomya | Representative species | EMP(1391F/EukBr)b,c | 563F/1132Rc | 574F/952Rc | 574*F/952Rc | 616*F/1132Rc | 1183F/1631Rc | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| V9 | V4–V5 | V4–V5 | V4–V5 | V4–V5 | V7–V8 | ||||||||
| 145 bp | 569 bp | 378 bp | 378 bp | 516 bp | 449 bp | ||||||||
| Nematoda (2169) | Roundworm, Filaria | 88.2 | (551/625) | 95.9 | (2072/2160) | 42.0 | (909/2163) | 93.2 | (2015/2163) | 96.0 | (2080/2166) | 88.0 | (1824/2072) |
| Platyhelminthes (1963) | Tapeworm, Fluke | 81.8 | (306/374) | 88.4 | (1713/1937) | 89.2 | (1734/1945) | 88.9 | (1729/1945) | 88.7 | (1727/1947) | 90.1 | (1713/1901) |
| Acanthocephala (63) | Spiny-headed worm | 100.0 | (26/26) | 95.2 | (60/63) | 0.0 | (0/63) | 0.0 | (0/63) | 93.7 | (59/63) | 0.0 | (0/62) |
| Coccidia (671) | Coccidium | 96.0 | (168/175) | 97.9 | (656/670) | 96.7 | (649/671) | 96.7 | (649/671) | 97.2 | (652/671) | 90.8 | (444/489) |
| Cryptosporida (55) | Cryptosporidium | 97.3 | (36/37) | 94.5 | (52/55) | 96.4 | (53/55) | 96.4 | (53/55) | 92.7 | (51/55) | 100.0 | (53/53) |
| Haemosporidia (149) | Plasmodium | 87.5 | (63/72) | 0.0 | (0/148) | 98.0 | (145/148) | 98.0 | (145/148) | 0.0 | (0/149) | 0.0 | (0/95) |
| Fornicata (21) | Giardia | 100.0 | (7/7) | 100.0 | (21/21) | 23.8 | (5/21) | 33.3 | (7/21) | 71.4 | (15/21) | 30.0 | (6/20) |
| Discicristata (909) | Trypanosoma, Leishmania | 92.2 | (306/332) | 93.0 | (806/867) | 68.0 | (608/894) | 69.9 | (663/949) | 71.7 | (640/893) | 86.2 | (698/810) |
| Parabasalia (303) | Trichomonas | 77.0 | (47/61) | 98.0 | (297/303) | 0.0 | (0/303) | 44.2 | (134/303) | 19.8 | (60/303) | 0.0 | (0/299) |
| Entamoebida (4) | Entamoeba | 100.0 | (3/3) | 100.0 | (4/4) | 100.0 | (4/4) | 100.0 | (4/4) | 100.0 | (4/4) | 0.0 | (0/3) |
| Longamoebia (158) | Acanthamoeba | 73.6 | (39/53) | 87.4 | (125/143) | 89.0 | (130/146) | 90.4 | (132/146) | 88.0 | (132/150) | 89.5 | (119/133) |
| Fungi (15101) | 56.4 | (3076/5458) | 96.6 | (14501/15006) | 45.3 | (1434/3164) | 95.6 | (14412/15071) | 93.7 | (14156/15100) | 91.9 | (13132/14290) | |
| Bacteria (575268) | 37.6 | (34016/90407) | 89.9 | (516999/58262) | <0.1 | (12/575261) | <0.1 | (14/575247) | <0.1 | (252/575265) | <0.1 | (1/558088) | |
| Euteleostomi (1091) | Mammald | 55.0h,m | (382/694) | 75.5h,m | (816/1081) | 72.5h,m | (784/1081) | 61.6h,m | (788/1081) | 75.0h,m | (815/1087) | 62.5h,m | (599/958) |
Primer sets were tested for matches to sequences in the SILVA database (v.132) using TestPrime under the following parameters: maximum number of mismatches of four bases and length of 0-mismatch at the 3′ end of three bases). TestPrime computes coverages for each taxonomic group by running in silico PCR on the SILVA database via sorting database sequences into “match”, “mismatch” and “nodata (sequences not covering the primer match position)”. The frequencies of “match” sequences among “match” and “mismatch” sequences are shown as percentages with the sequence numbers in parentheses.
aNumbers in parentheses show the numbers of sequences available in the SILVA database. Please note these numbers are not always the denominators because of the presence of “nodata” sequences.
bOnly 17 bases from 3′ was used for the primer EukBr because many sequences in the SILVA database lacks the corresponding 5′ region.
cTarget variable regions and amplicon sizes based on the S. cerevisiae rRNA gene (NC_001144) are shown below the primer names.
dPrimer match to humans and mice is indicated by superscripts h and m on the values, respectively.