For instance, efficiency in dairy cattle has doubled in the last 50 years, even though feed efficiency has not been directly selected for. Feed efficiency has been traditionally improved via enhanced diets, and genetic selection to produce more milk per live weight. Feed efficiency is one of the most important characteristics in cattle due to its relationship with farm benefits, but also because its impact on securing food for a growing human population, decreased land use, or mitigation of greenhouse gas emissions. However, few studies have associated feed efficiency traits to whole metagenome sequences, and their results have not yet been validated 5. There are previous international collaborations that aim to assemble the rumen metagenome in order to provide more comprehensive information on the microorganisms that populate the cow rumen 17, 18, 19, 20. Besides, different taxonomical groups may be involved in similar functions, hiding true association at the gene function level when only looking at the taxonomical composition. This strategy provides limited information because reads must be aligned against incomplete databases that lack of specific rumen microbes. Most of these studies used 16S rRNA sequencing as a description of the microbiota. Previous studies have related well-known taxonomical groups or community composition with feed efficiency or residual feed intake (RFI) 8, 15, 16. Depending on the microbiota composition, the input nutrients (feed) are transformed in an output product (milk) in a more or less efficient manner. In the year 2018, the rumen microbiome is estimated to be responsible for digesting around ten thousand million tons of cellulosic material worldwide to provide milk and meat for 7.6 billion people 14. In cattle in particular, the rumen microbiota is known to be associated with feed digestion and availability of nutrients for the host. Microbiome research is gaining attention in livestock species, as it assists on understanding diseases and efficiency processes that occur in animals.
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Furthermore, links have been observed between the host genotype and the gastrointestinal microbial composition 8, 10, 11, 12, 13, proving that the microbial communities that populate the individual digestive niches are not only dependent on environment and diet, but also on the host genotype. Recent research has proposed the microbiota as a proxy or phenotype to predict complex traits, such as body mass index in humans or feed efficiency in livestock animals 5, 8, 9, 10. Under certain dysbiosis, it can cause diseases and underperformance 3, 4, 5, 6, 7. The microbiome can be considered as a holobiont organism that populates different niches in mammals and interacts with the host, in most cases, in a symbiotic manner such as during the digestion of feed, or modulating the immune response 1, 2. Some of these differences remain even between populations under different diets and environments, and can provide information on the feed utilization performance without information on the individual intake level. These differences are even more evident in terms of intake levels. The findings indicated that there are differences between the microbiota compositions of high and low-efficiency animals both at the taxonomical and gene levels. Enrichment analyses showed that genes within these contigs were mainly involved in fatty acids and cellulose degradation pathways. Nonetheless, a larger potential accuracy up to 0.69 was foreseen in this study for datasets that allowed a larger statistical power. These microbial contigs were also able to predict FE and intake levels with accuracy of 0.19 and 0.39, respectively, in an independent population (n = 31). An agnostic pre-selection of microbial contigs allowed high classification accuracy for FE and intake levels using hierarchical classification.
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A de novo metagenome assembly was carried out using de Bruijn graphs in MEGAHIT resulting in 496,375 contigs.
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Methanobacteria (P = 0.004) and Methanobrevibacter (P = 0.003) were also less abundant in the high-efficiency cows. This study revealed that most efficient cows had larger relative abundance of Bacteroidetes (P = 0.041) and Prevotella (P = 0.003), while lower, but non-significant (P = 0.119), relative abundance of Firmicutes. Modulating the microbiota composition can promote a more sustainable and efficient livestock. The variability for the efficiency of feed utilization in ruminants is partially controlled by the gastrointestinal microbiota. Improving feed efficiency (FE) is important for a more sustainable livestock production. The current research was carried out to determine the associations between the rumen microbiota and traits related with feed efficiency in a Holstein cattle population (n = 30) using whole metagenome sequencing.