Characterizing the Composition of the Rumen Microbiome: A DNA Metabarcoding Approach

The rumen microbiome plays a central role in the ability of ruminants to digest plant material, which has major implications for nutrient supply to the animal and for production of fermentation end-products such as methane. Therefore, we need a more comprehensive understanding of the factors influencing rumen taxonomic composition, including host genome and diet. Here, we present a DNA metabarcoding approach to characterize the taxa of bacteria, archaea, fungi and protozoa present in the rumen. DNA metabarcoding consists in:

1. amplifying short DNA fragments (“barcodes”) from a complex mixture of organisms using primers specifically designed for a particular taxonomic group of interest;
2. sequencing these barcodes using next-generation sequencing technologies; and
3. assigning the obtained sequences to the corresponding taxa based on a reference sequence database.

In this study, we designed the most efficient primer pairs to amplify each rumen target taxon. For this purpose, we drew upon publicly available sequence data, while taking into consideration current next-generation sequencing constraints. Then we illustrated the usefulness of DNA metabarcoding in an experiment investigating the influence of the host species on the rumen microbiome ecosystem, where rumen contents have been transferred from cows to reindeers and sampled periodically afterwards.