Shallow shotgun metagenomic functional analysis
In contrast to 16S amplicon data, shallow shotgun metagenomic data also
provide direct estimates of microbiome functional potential. Horses
without access to sandwort had greater relative abundances of reads
which mapped to genes related to cellulases, enzymes which break down
cellulose (the primary structural component of plant cell walls) into
monosaccharides. Horses without access to sandwort were also enriched in
metabolic pathways for pyruvate fermentation to acetate (and S-lactate).
In horses, acetate is the primary fatty acid produced at the end of a
metabolic chain which begins with the lysis of plant fibres .
Conversely, metabolic pathways for sucrose and host glycan
(N-Acetylneuraminic acid) degradation were enriched among horses with
access to sandwort, alongside genes for amylase and fructosidase
synthesis. Compared to taxonomic patterns, these functional results more
directly support our hypothesis that sea sandwort consumption reduces
fibrolytic niche space in the microbiome, and shifts communities towards
the metabolism of simple sugars and host glycans.
Contrary to taxonomic indicators, we did not observe an association
between oxalate decarboxylase genes and horse access to sandwort.
Although reads which mapped to oxalate decarboxylase genes were
observed, they were present at low abundances (< 10 reads) and
not observed in all samples. This highlights a limitation of shallow
shotgun sequencing. While shallow shotgun sequencing may be sufficient
to detect patterns in genes which are abundant and widely distributed in
the microbiome, genes related to specialized functions which are only
found in a rare subset of taxa may require deep shotgun metagenomic
sequencing or targeted sequencing.