Comparisons of sequencing depth
We sought to test the ability of shallow shotgun sequencing to
accurately characterize gut microbiome variation in the Sable Island
feral horse population and whether it could recapitulate biological
patterns observed in a twinned 16S rRNA gene amplicon dataset. We
observed that sequencing depths at the scale of hundreds of thousands of
read pairs yielded near identical patterns in microbiome alpha and
beta-diversity as more deeply sequenced datasets. Similar results were
observed with respect to HUMANn3 based estimates of MetaCyc pathway and
reaction relative abundances. While not a synonymous substitution for
deep shotgun sequencing, like previous studies , we conclude that
shallow shotgun metagenomic sequencing can accurately estimate major
biological patterns in the microbiome.