Conclusion
We demonstrated that shallow shotgun sequencing yields characterization
of the Sable Island horse microbiome which is comparable to both deeper
shotgun sequencing (when using a read-based profiler) and 16S rRNA gene
amplicon datasets. Shallow shotgun sequencing also replicated biological
patterns reported in a previously published amplicon dataset, while also
providing estimates of microbiome functional potential. Amplicon data
may be better suited for some research questions; for example, those
pertaining to biological patterns which are hypothesized to be the
result of microbiota dispersal. However, the assembly of system-specific
MAGs may help to narrow this gap. Researchers should still seek to
validate shallow shotgun sequencing for their own study systems,
especially if microbiota in their systems are likely to be
underrepresented in genome databases. But, based on data from Sable
Island feral horse fecal samples, we conclude that shallow shotgun
sequencing can provide greater biological insight than amplicon data, at
a comparable cost, and with greater long-term value.