Comparison of library preparation methods
Next, using a 13-sample dataset, we compared sequencing results
generated using a prevailing library preparation technique (Illumina
Nextera XT) with those created using a new commercially available method
which allows for high-throughput preparation at a lower per-sample-price
(iGenomx Riptide). Estimates of Shannon diversity between the Nextera XT
and iGenomx Riptide generated datasets (both rarefied to 1.6 million
bacterial read pairs per sample) were highly correlated
(R2 = 0.98, t = 22.988, p< 0.01). Shannon diversity estimates tended to be lower among
the sequenced iGenomx Riptide libraries, but this effect was
non-significant (t = -1.953 p = 0.08). Bray-Curtis
estimates of beta-diversity were also correlated between Nextera XT and
iGenomx Riptide created datasets (mantel: r = 0.86, p< 0.01; Figure 3A), as were log-transformed species-level
estimates of taxa relative abundances (R2 =
0.97, t = 1121.42, p < 0.01; Figure 3B).