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 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 demonstrate how shallow
shotgun metagenomic data also provided useful insights about microbiome
functional potential which support previously hypothesized diet effects
in this study system.