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Diet Assessment Based on Rumen Contents: A Comparison between DNA Metabarcoding and Macroscopy
- Source :
- PLoS ONE, Vol 11, Iss 6, p e0157977 (2016), PLoS ONE
- Publication Year :
- 2016
- Publisher :
- Public Library of Science (PLoS), 2016.
-
Abstract
- Dietary choices are central to our understanding of ecology and evolution. Still, many aspects of food choice have been hampered by time consuming procedures and methodological problems. Faster and cheaper methods, such as DNA metabarcoding, have therefore been widely adopted. However, there is still very little empirical support that this new method is better and more accurate compared to the classic methods. Here, we compare DNA metabarcoding to macroscopic identifications of rumen contents in two species of wild free-ranging ungulates: roe deer and fallow deer. We found that the methods were comparable, but they did not completely overlap. Sometimes the DNA method failed to identify food items that were found macroscopically, and the opposite was also true. However, the total number of taxa identified increased using DNA compared to the macroscopic analysis. Moreover, the taxonomic precision of metabarcoding was substantially higher, with on average 90% of DNA-sequences being identified to genus or species level compared to 75% of plant fragments using macroscopy. In niche overlap analyses, presence/absence data showed that both methods came to very similar conclusions. When using the sequence count data and macroscopic weight, niche overlap was lower than when using presence-absence data yet tended to increase when using DNA compared to macroscopy. Nevertheless, the significant positive correlation between macroscopic quantity and number of DNA sequences counted from the same plant group give support for the use of metabarcoding to quantify plants in the rumen. This study thus shows that there is much to be gained by using metabarcoding to quantitatively assess diet composition compared to macroscopic analysis, including higher taxonomic precision, sensitivity and cost efficiency.
- Subjects :
- Computer and Information Sciences
Rumen
Molecular biology
lcsh:Medicine
Artificial Gene Amplification and Extension
Plant Science
Polymerase Chain Reaction
Sequencing techniques
Medicine and Health Sciences
Animals
DNA Barcoding, Taxonomic
lcsh:Science
DNA sequence analysis
Taxonomy
Data Management
Nutrition
Probability
Mammals
Ecology
Deer
Ecology and Environmental Sciences
lcsh:R
Organisms
Sequence analysis
Biology and Life Sciences
Plant Taxonomy
Ruminants
Sequence Analysis, DNA
Trophic Interactions
Diet
Research and analysis methods
Molecular biology techniques
Community Ecology
Food
Vertebrates
Amniotes
lcsh:Q
Ecological Niches
Research Article
Subjects
Details
- Language :
- English
- ISSN :
- 19326203
- Volume :
- 11
- Issue :
- 6
- Database :
- OpenAIRE
- Journal :
- PLoS ONE
- Accession number :
- edsair.pmid.dedup....a82579d581d72e18c38511466b3ecd2a