Data from: Comparing the effectiveness of metagenomics and metabarcoding for diet analysis of a leaf-feeding monkey (Pygathrix nemaeus)

Fecal samples are of great value as a non-invasive means to gather
information on the genetics, distribution, demography, diet, and parasite
infestation of endangered species. Direct shotgun sequencing of fecal DNA
could give information on these simultaneously, but this approach is
largely untested. Here we use two fecal samples to characterize the diet
of two Red-Shanked Doucs Langurs (Pygathrix nemaeus) that were fed a known
combination of foliage, fruits, vegetables and cereals. Illumina HiSeq
sequencing produced ~70 million paired reads per sample, of which ~10000
(0.014%) and ~44000 (0.066%) respectively corresponded to chloroplast
genomes. Sequences were matched against a database of available
chloroplast ‘barcodes’ for angiosperms. The results were compared with
‘metabarcoding’ using PCR amplification of the P6 loop of trnL. Shotgun
sequencing identified 7 and 9 of the likely 16 diet plants, against 6 and
5 plant species identified by metabarcoding. Metabarcoding produced
thousands of reads that were consistent with the known diet, but the
barcodes were too short to identify several diet plants to genus.
Metagenomics could utilize multiple, longer barcodes that combined had
greater power of identification, but rare diet items were not recovered.
Read numbers for diet species in metagenomic and metabarcoding data were
correlated, indicating that both approaches are useful for determining
relative sequence abundance. Metagenomic reads were uniformly distributed
across the chloroplast genomes; thus if chloroplast genomes were to be
used as reference, the precision of identifications and species recovery
would improve further. Metagenomics also recovered the host mitochondrial
genome and numerous intestinal parasite sequences in addition to
generating data useful for characterizing the microbiome.