Data from: A pipeline for metabarcoding and diet analysis from fecal samples developed for a small semi-aquatic mammal

Metabarcoding allows the genetic analysis of pooled samples of various
sources. It is becoming popular in the study of animal diet, especially
because it allows the analysis of the composition of feces without the
need of handling animals. In this work, we studied the diet of the
Pyrenean desman (Galemys pyrenaicus), a small semi-aquatic mammal endemic
to the Iberian Peninsula and the Pyrenees, by sequencing COI minibarcodes
from feces using next-generation sequencing techniques. For the
identification of assembled sequences, we employed a tree-based
identification method that used a reference tree of sequences of
freshwater organisms. The comparison of freshly collected fecal samples
and older samples showed that fresh samples produced significantly more
sequencing reads. They also rendered more operational taxonomical units
(OTUs), but not significantly. Our analyses of 41 samples identified 224
OTUs corresponding to species of the reference tree. Ephemeroptera,
Diptera excl. Chironomidae, and Chironomidae were the most highly
represented groups in terms of reads as well as samples. Other groups of
freshwater organisms detected were Plecoptera, Trichoptera, Neuropteroida,
Coleoptera, Crustacea, and Annelida. Our results are largely in line with
previous morphological and genetic studies on the diet of the Pyrenean
desman, but allowed the identification of a higher diversity of OTUs in
each sample. Additionally, the bioinformatic pipeline we developed for
deep sequencing of fecal samples will enable the quantitative analysis of
the diet of this and other species, which can be highly useful to
determine their ecological requirements.