What's inside a rumen?

Roe deer fawn (Capreolus capreolus)

Many central questions in ecology focus on the use and selection of food by individuals, populations or species. Particularly, in large herbivores the applications of such knowledge of the diet is wide ranging. For example, management related questions and the consequences for commercially valuable crops and trees are dependent on knowledge about diets. Most studies of wild ungulate diets use traditional techniques such as macroscopic ruminal, or histological fecal analysis. However these techniques are hampered with inherent methodological problems that involve inaccurate determination of fragmented plant material or simply missing the very small fragments.

This likely introduces bias related to digestibility. Some food items are digested faster than other components and often the latter remain the only identifiable bits for macroscopical ruminal analysis. Quantitative comparisons of diet components based on such analyses will only be of limited used for interpretations of relative importance of food items. In a new studies colleagues compared "metabarcoding" to macroscopic identifications of rumen contents in two species of wild free-ranging ungulates. I set the term metabarcoding in quotation marks simply because the authors did not use a standard plant barcode marker but rather the trnL (UAA) intron. The locus has been used successfully in the past but it is not a DNA barcode.

The authors used Ion Torrent PGM system to analyze diet composition based on rumen content from two large herbivores living in sympatry, roe deer (Capreolus capreolus) and fallow deer (Dama dama), and compared it to a classical macroscopic method to determine food items.

Overall we found a greater number of identified taxa when using DNA. This may reflect the fact that food material stays in the rumen for only a few hours before it is ruminated and later passed along to the stomach. Thus, after rumination some plant species might become unidentifiable macroscopically, while they still are detectable using DNA. Thus, using DNA methods may also increase the window of time for detection of some food items. 

Overall, the high-throughput sequencing data did prove to be more sensitive and taxonomically more reliable. More taxa could be identified and it showed a positive correlation with the amount of biomass identified traditionally, suggesting that the number of DNA sequences obtained may be used as an indicator for how much biomass was consumed.