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.