Abstract
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.