Investigations into the deer rumen microbiome

Grazing ruminants are able to digest complex starches such as plant cell walls through a symbiotic relationship with microbes that inhabit the fore-stomach or ‘rumen’. Fermentation pathways and the resulting energy sources and waste products differ depending on the microbial community in the gut. Although diet is the main driver, Rumen microbial communities (RMC) have been shown to be affected by the host genetics and to be heritable in sheep and cattle and are predictive of feed related traits such as methane emissions, a by-product of the fermentation process. The aim of this project was to determine the variability in RMC amongst individual deer and to estimate heritability of the deer RMC. The rumen content of 853 red and wapiti cross deer were sampled, and microbial DNA was sequenced using restriction enzymes reduced representation sequencing, which is a reduced sampling method that captures ~1% of the microbial genomes. A genome taxonomy database was used to determine taxonomy assignment. Sequences were used to determine similarity of RMC amongst individuals and presence of known microbes. Contemporary group, herd and farm were shown to significantly affect RMC composition. Similar to other ruminants, Prevotella overall was the most abundant genera present in the rumen. Similarly, Sodaliphilus, a genus linked to increased methane production is found in the top 10 most abundant microbial genera across the samples examined. The heritability of the RMC was estimated by using principal component analysis for dimension reduction. Heritability estimates were ~3% (+/- (6.150%). These were lower than reported in other species. Next steps are to determine whether there are components of the RMC that are unique to deer and associations with key production traits such as growth and methane emissions.

MapNet abstract title: Investigating Rumen Microbial Communities in New Zealand farmed deer