Shallow shotgun sequencing of the microbiome recapitulates 16S amplicon results and provides functional insights

Prevailing 16S rRNA gene-amplicon methods for characterizing the bacterial
microbiome of wildlife are economical, but result in coarse taxonomic
classifications, are subject to primer and 16S copy number biases, and do
not allow for direct estimation of microbiome functional potential. While
deep shotgun metagenomic sequencing can overcome many of these
limitations, it is prohibitively expensive for large sample sets. We
evaluated the ability of shallow shotgun metagenomic sequencing to
characterize taxonomic and functional patterns in the fecal microbiome of
a model population of feral horses (Sable Island, Canada). Since 2007,
this unmanaged population has been the subject of an individual-based,
long-term ecological study. Using deep shotgun metagenomic sequencing, we
determined the sequencing depth required to accurately characterize the
horse microbiome. In comparing conventional versus high-throughput shotgun
metagenomic library preparation techniques, we validate the use of more
cost-effective lab methods. Finally, we characterize similarities between
16S amplicon and shallow shotgun characterization of the microbiome and
demonstrate that the latter recapitulates biological patterns first
described in a published amplicon dataset. Unlike amplicon data, we
further demonstrate how shallow shotgun metagenomic data provide useful
insights about microbiome functional potential which support previously
hypothesized diet effects in this study system.