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Table 4 Advantages and disadvantages between blocking and excluding primers to study protists within oyster microbiota

From: Unveiling protist diversity associated with the Pacific oyster Crassostrea gigas using blocking and excluding primers

 

18SV4BP

UNonMet

18SV1V2EX

Advantages

BP specifically targets host sequences

No host sequences are expected to be amplified

No host sequences were amplified

Protist diversity is expected to be well represented

High nucleotide polymorphism compared to 18SV4BP

Disadvantages

Host sequences were not completely removed

Excluding primers might not only exclude metazoans, but also other unexpected taxa

Expected amplicon size is too large for current Illumina MiSeq technology

 

Low nucleotide polymorphism compared to 18SV1V2EX