High-throughput DNA sequencing of the moose rumen from different geographical locations reveals a core ruminal methanogenic archaeal diversity and a differential ciliate protozoal diversity.

Moose rumen samples from Vermont, Alaska and Norway were investigated for methanogenic archaeal and protozoal density using real-time PCR, and diversity using high-throughput sequencing of the 16S and 18S rRNA genes. Vermont moose showed the highest protozoal and methanogen densities. Alaskan samples had the highest percentages of , followed by the Norwegian samples. One Norwegian sample contained 43 % , whilst all other samples contained < 10 %. Vermont samples had large percentages of , as did two Norwegian samples. represented one-third of sequences in three samples. Samples were heterogeneous based on gender, geographical location and weight class using analysis of molecular variance (AMOVA). Two Alaskan moose contained >70 % and one contained >75 % spp. Protozoa from Norwegian moose belonged predominantly (>50 %) to the genus , especially . Norwegian moose contained a large proportion of sequences (25-97 %) which could not be classified beyond family. Protozoa from Vermont samples were predominantly (>75 %), with up to 7 % . Four of the eight Vermont samples also contained 5-12 % spp. Samples were heterogeneous based on AMOVA, principal coordinate analysis and UniFrac. This study gives the first insight into the methanogenic archaeal diversity in the moose rumen. The high percentage of rumen archaeal species associated with high starch diets found in Alaskan moose corresponds well to previous data suggesting that they feed on plants high in starch. Similarly, the higher percentage of species related to forage diets in Vermont moose also relates well to their higher intake of fibre.