Elucidating bovine host genomic links with rumen microbial genes to improve sustainably feed conversion efficiency using unique selection criteria

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Rumen microbial fermentation confers a unique ability to convert human inedible feed into foods with high nutritional value (e.g. meat, milk), but produces the Greenhouse Gas methane. The overall aim is to unravel the host genetic control of its rumen microbiome (here identified as rumen microbial gene abundances (RMGA)) affecting feed conversion efficiency (FCE) and methane emissions. This will rectify the major knowledge gap about these complex interactions, as well as providing the basis to develop selection criteria and breeding strategies for improvement of FCE and mitigation of methane emissions. Our industrial partner Genus plc has a large, well-structured, genotyped, phenotyped and rumen sampled cattle population to be used as data source to estimate these complex interactions. To determine RMGA in a cost effective way, we will develop a functional microbial gene microarray (FMGM). The FMGM will include genes associated with FCE and methane emissions based on results from the whole metagenomic sequencing work.. Probes specific to ruminant Proteobacteria, Firmicutes, and Bacteroidetes will be included on the FMGM to use their ratio as biomarker for rumen dysbiosis and health. The host genomic effect on the microbiome-phenotype interactions will be estimated using REML and Bayesian analysis. The microbiome-phenotype interactions will be identified using network, partial least squares and random forest regression analyses. Functional pathway analysis will be applied to identify the functional causes of the interactions among RMGA. These functional analyses will give insight into the 'cross-talk' between the rumen microbiome and host. All findings from the analyses of the host genome-microbiome-phenotype interactions will be combined to develop novel selection criteria to breed animals based on RMGA associated with FCE and methane emissions without the need for very costly trait measurements.

The Food and Agriculture Organisation of the United Nations has predicted an increase in global meat and milk demand of 76% and 63% by 2050 due to increasing income and growing world population. This will require improved sustainable systems for livestock production. The large fore-gut of cattle, the rumen, contains billions of microbes (the microbiome) per gram of digesta (which is the substance as food undergoes digestion). These microbes ferment human inedible food (e.g. grass) into nutrients the host animal converts into high quality products such as meat and milk. This rumen microbial eco-system is essential for the animal but has one disadvantage for the environment because some microbes produce the potent greenhouse gas methane. This project will address these challenges by using rumen microbial information as animal breeding criteria for improvement of feed conversion efficiency with simultaneous mitigation of methane emissions. In this research we will estimate the extent of the link between animal genome and its rumen microbiome and investigate the causes for their link using a large breeding population. This population is provided by our commercial partner Genus plc and is well structured to ensure accurate estimation of host genetic effects on the microbiome. Our previous research showed that rumen microbial gene abundances are closely related to feed conversion efficiency and methane emissions. However, how and to what extent the host animal genome affects the abundances of microbial genes is unknown and will be investigated within this project. Because the metabolic functions of these microbial genes are mostly known, we expect to identify many novel genetic links between the host animal and specific rumen microbial functions that may even be conserved across species. Networks and functional pathways of rumen microbial genes linked to the animal genome will provide a new level of understanding of the symbiosis between microbiome and host animal. We are expecting to identify pathways of microbial genes, e.g. to provide insight into the "cross-talk" between the rumen microbes and the host animal, being a route by which the host genome controls its own rumen microbiome. Based on these findings, optimised selection criteria and strategies to improve feed conversion ratio and mitigate methane emissions will be developed. In addition, we will use biomarkers to control that there are no adverse effects of selection using microbial genes on rumen health with potential consequences for animal health and welfare. Our large commercial partner will ensure that the outcomes of the project can be immediately implemented in the routine breeding activities and thus contribute to address the challenges of food security and environmental impact of animal production. This project is expected to provide an enormous increase in fundamental knowledge of the links between host animal genome and the rumen microbiome, which may be also relevant in other species including humans, and at the same time will develop methods and strategies to use this new knowledge for practical application in animal breeding.