Table 1.

Identification of species from OTUs using BLAST (basic local alignment search tool)

Best species match from BLAST search	Query cover	Identity	Number of samples	OTU Sequence length	Number of sequence reads
Chabertia ovina	100	100	37	283	8,418
Haemonchus contortus	100	100	127	281	102,110
Teladorsagia circumcincta	100	99	80	296	28,293
Trichostrongylus vitrinus	100	100	40	288	10,311
Oesophagostomum venulosum	99	100	20	308	3,288
Bunostomum trigonocephalum	100	100	3	281	199
Cooperia curticei	100	99	1	292	800
Cooperia oncophora	100	100	5	291	1,290
Coronocyclus coronatus	100	99	1	281	735
Cylicocyclus nassatus	100	98	10	370	1,294
Cylicostephanus minutus	99	100	3	266	200
Cystocaulus ocreatus	100	99	3	418	85
Muellerius capillaris	100	100	2	455	35
Ostertagia leptospicularis	100	99	1	289	66
Ostertagia ostertagi	100	100	3	288	364
Varestrongylus eleguneniensis	94	100	2	411	23

The top five species represent 97% of the reads. Nematodes were identified in 156 (99%) out of 158 larval culture samples. The most common species was Haemonchus contortus, which was identified in 127 (80%) of the positive samples and was also represented by most of the sequence reads across all samples. The ITS2 fragments for all OTUs varied in length from 266 to 455 bp