Rumen microbial populations in grain and roughage fed Merino ewes assessed using two sampling methods

In this study, the microbial populations in the rumen fluid of Merino ewes fed grain or roughage diets were investigated using two different rumen collection methods: percutaneous needle aspiration (rumenocentesis) and oral stomach tube. There was no difference in the bacterial species found between the two rumen collection methods. Total ciliate numbers (entodiniomorphs and holotrichs) did not differ between diets. However, the number of holotrichs, which accounted for 2-4% of the total ciliates, was higher in the rumen fluid from grain-fed ewes compared to roughage-fed ewes. The analyses of microbiomes showed that the rumen bacterial species in grain-fed ewes differed considerably from the rumen bacteria in roughage-fed ewes. There was a total of 532 operational taxonomic units identified, and a differential relative abundance between the two diets was found for 166 bacterial taxa. The differences in the microbial abundance between the two diets found at the genus level provides a detailed understanding of the effects of diet on rumen microbial communities in Merino sheep.