Abstract
In this study, Bos Taurus cattle offered one high concentrate diet (92% concentrate-8% straw) during two independent trials allowed us to classify 72 animals comprising of two cattle breeds as “Low” or “High” feed efficiency groups. Digesta samples were taken from individual beef cattle at the abattoir. After metagenomic sequencing, the rumen microbiome composition and genes were determined. Applying a targeted approach based on current biological evidence, 27 genes associated with host-microbiome interaction activities were selected. Partial least square analysis enabled the identification of the most significant genes and genera of feed efficiency (VIP > 0.8) across years of the trial and breeds when comparing all potential genes or genera together. As a result, limited number of genes explained about 40% of the variability in both feed efficiency indicators. Combining information from rumen metagenome-assembled genomes and partial least square analysis results, microbial genera carrying these genes were determined and indicated that a limited number of important genera impacting on feed efficiency. In addition, potential mechanisms explaining significant difference between Low and High feed efficiency animals were analyzed considering, based on the literature, their gastrointestinal location of action. High feed efficiency animals were associated with microbial species including several Eubacterium having the genetic capacity to form biofilm or releasing metabolites like butyrate or propionate known to provide a greater contribution to cattle energy requirements compared to acetate. Populations associated with fucose sensing or hemolysin production, both mechanisms specifically described in the lower gut by activating the immune system to compete with pathogenic colonizers, were also identified to affect feed efficiency using rumen microbiome information. Microbial mechanisms associated with low feed efficiency animals involved potential pathogens within Proteobacteria and Spirochaetales, releasing less energetic substrates (e.g., acetate) or producing sialic acid to avoid the host immune system. Therefore, this study focusing on genes known to be involved in host-microbiome interaction improved the identification of rumen microbial genetic capacities and potential mechanisms significantly impacting on feed efficiency in beef cattle fed high concentrate diet.
Highlights
The FAO predicted that by 2050, the human population will grow to over 9 billion people, and in the same time frame, global meat consumption is projected to increase by 73% (FAO, 2019)
“High” animals have a low feed conversion ratio (FCR) and residual feed intake (RFI) values meaning they are efficient to convert feed into live weight gain, whilst “Low” animals performing in the opposite way
All animals offered concentrate diet were selected and showed significant differences between groups of animals based on FCR or RFI (Figure 1), confirming the grouping selection based on feed efficiency indicators and balanced for year of the trial and breed (Supplementary Table S1)
Summary
The FAO predicted that by 2050, the human population will grow to over 9 billion people, and in the same time frame, global meat consumption is projected to increase by 73% (FAO, 2019). Intensive food production using more concentrate diet instead of forage improved feed efficiency in ruminant production, reducing methane emissions, it generated a stress on the rumen microbiome and the animal (Auffret et al, 2017; Wetzels et al, 2017). Both studies confirmed the influence of concentrate over forage diets to generate rumen dysbiosis in beef and dairy cattle. This disturbance is explained by a breach of robustness in microbiome composition and functionality associated with a “bloom” of zoonotic pathogens especially within Proteobacteria, as found in humans (Brown et al, 2012)
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