Heterogeneity Primer Spacers Improve the Performance of Massively Parallel Amplicon Sequencing of the V3-V4 Region of the 16 S rDNA as well as the 18 S Region for Blastocystis Subtyping

The Illumina MiSeq and NextSeq instruments are workhorses for many low- to medium-throughput amplicon sequencing applications in microbiology; however, their performance is highly sensitive to decreased diversity of libraries. Here, we present a systematic, algorithm-driven approach to designing heterogeneity spacers for amplification primers and demonstrate their use in two marker gene profiling applications. Heterogeneity spacers were designed to balance the sequencing signal, ensuring that no sequencing cycle contained more than 60% of a single dominant base. Additional bases were inserted into the first-round amplification primer adjacent to the target-specific portion. A simple script was written to remove the heterogeneity spacers from the reads, and verify equal representation of primer combinations. We designed sixteen staggered primer variants for profiling the V3-V4 regions of the 16S bacterial rDNA gene and sixteen for bidirectional profiling of the 18S rDNA region informative for Blastocystis subtypes. The effectiveness of our design was evident from the increased heterogeneity of the sequencing signal, with no primer combination predominating. The method was tested against classical primer design and has successfully been applied to several thousand samples to date. Inserting heterogeneity spacers before the target-specific portion of the first-round PCR primers is a simple and reliable way to increase the diversity of marker gene amplicons. The multiplexed reactions produce amplicons that can be easily sequenced on Illumina platforms, eliminating the need for high concentrations of balancing PhiX library.