An integrated multi-omics approach reveals the effects of supplementing grass or grass hay with vitamin E on the rumen microbiome and its function

Rumen function is generally sub-optimal leading to losses in the form of methane and nitrogen. Analysis of the rumen microbiome is thus important to understand underlying microbial activity under different feeding strategies. This study investigated the effect of forage conservation method and vitamin E supplementation on rumen function using the rumen simulation technique (Rusitec). Dietary treatments consisted of ryegrass (GRA) or ryegrass hay (HAY) supplemented with 20% concentrate containing zero or 50 IU/d vitamin E, as a-tocopheryl acetate, according to a 2×2 factorial design. Forage conservation method did not substantially change the nutrient composition but had a profound impact on the structure and diversity of the main rumen microbial communities. HAY diets promoted a more complex bacterial community (+38 OTUs) dominated by Firmicutes. This adaptation, together with increased rumen protozoa levels and greater diversity in the bacterial and methanogen communities, led to greater fibre degradation (+12%) in HAY diets, but also to greater proteolysis (+15%) than observed with GRA diets. Inter-species H transfer between fibrolytic bacteria, protozoa and methanogens was greater in HAY diets, which resulted in higher metabolic H recovery and ultimately higher methane emissions (+35%). On the contrary, GRA diets promoted more simplified methanogen and bacterial communities. This bacterial community was dominated by Bacteroidetes and Lactobacillus, thus lactate formation may have acted as an alternative H sink in GRA diets. Moreover the structure of the bacterial community with GRA diets was highly correlated with N utilization, and GRA diets promoted greater bacterial growth and microbial protein synthesis (+16%), as well as a more efficient microbial protein synthesis (+22%). A dose-response experiment using batch cultures revealed that a-tocopheryl acetate was more effective than a-tocopherol in improving rumen fermentation, moreover a high vitamin E dose (500 IU/L) had a negative impact on rumen function. This improvement consisted of a small increase in feed degradability (+8%), possibly as a result of the antioxidant properties of vitamin E which led to higher bacterial and protozoal levels. Moreover, vitamin E supplementation promoted substantial changes in the methanogen community suggesting that some methanogen species are particularly sensitive to oxidative stresses. Our findings suggested that when possible grass should be fed instead of grass hay, in order to improve rumen function and to decrease the environmental impact of livestock agriculture.