Fecal metagenomics for the simultaneous assessment of diet, parasites, and population genetics of an understudied primate.
BACKGROUND
Rapid habitat loss and degradation are responsible for population decline in a growing number of species. Understanding the natural history of these species is important for designing conservation strategies, such as habitat enhancements or ex-situ conservation. The acquisition of observational data may be difficult for rare and declining species, but metagenomics and metabarcoding can provide novel kinds of information. Here we use these methods for analysing fecal samples from an endangered population of a colobine primate, the banded leaf monkey (Presbytis femoralis).


RESULTS
We conducted metagenomics via shotgun sequencing on six fecal samples obtained from a remnant population of P. femoralis in a species-rich rainforest patch in Singapore. Shotgun sequencing and identification against a plant barcode reference database reveals a broad dietary profile consisting of at least 53 plant species from 33 families. The diet includes exotic plant species and is broadly consistent with > 2 years of observational data. Metagenomics identified 15 of the 24 plant genera for which there is observational data, but also revealed at least 36 additional species. DNA traces for the diet species were recovered and identifiable in the feces despite long digestion times and a large number of potential food plants within the rainforest habitat (>700 species). We also demonstrate that metagenomics provides greater taxonomic resolution of food plant species by utilizing multiple genetic markers as compared to single-marker metabarcoding. In addition, full mitochondrial genomes of P. femoralis individuals were reconstructed from fecal metagenomic shotgun reads, showing very low levels of genetic diversity in the focal population, and the presence of gut parasites could also be confirmed. Metagenomics thus allows for the simultaneous assessment of diet, population genetics and gut parasites based on fecal samples.


CONCLUSIONS
Our study demonstrates that metagenomic shotgun sequencing of fecal samples can be successfully used to rapidly obtain natural history data for understudied species with a complex diet. We predict that metagenomics will become a routinely used tool in conservation biology once the cost per sample reduces to ~100 USD within the next few years.
Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543 Singapore ; Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, SL5 7PY UK ; Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD UK.
Amrita
A
Srivathsan
Department of Anthropology, University of Colorado Boulder, Boulder, CO 80302 USA.
Andie
A
Ang
Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, SL5 7PY UK ; Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD UK.
Alfried P
AP
Vogler
Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543 Singapore ; Lee Kong Chian Natural History Museum, 2 Conservatory Drive, Singapore, 117377 Singapore.
Rudolf
R
Meier
Banded leaf monkeys; Colobines; Diet analyses; Metabarcoding; Metagenomics