Rumen metatranscriptomics of Nelore and its relation with performance in confinement

Description:
The complex microorganism community (bacteria, archaea and eukaryotes) present in the rumen is responsible for transforming low-quality foods, such as grass and foliage, into high-quality animal protein (meat and milk) through microbial fermentation. The communities of microorganisms associated with a host, or an environment, are known as microbiota. Studying the microbiome related to fermentation in ruminants can help to optimize the conversion of animal protein. However, most species present in the rumen cannot be cultivated, which makes the study of these microorganisms difficult. Advances in science, especially in the areas of molecular biology, biotechnology and bioinformatics, have opened paths for the studies of the ruminal microbiome that can bring genetic information about these species. In this scenario, Metagenomics and Metatranscriptomics have been implemented to try to address some gaps and deepen the knowledge of the microbiome in order to try to promote greater feed efficiency in cattle and thus enhance the conversion of animal protein. However, the current literature is focused on elucidating the taxonomy of the microorganisms present in the rumen and not looking to establish links between the microbial metabolic functions of the rumen. In this sense, we note a gap to be explored since integrative analysis can help to understand phenotypes. Therefore, this project aims, through the integration of experimental data from total RNA and miRNA, to expand the description of genomic regulatory elements and genes associated with phenotypes. For this purpose, this project will analyze the gene expression profile of the rumen microbiome of 52 Nellore. The animals were divided into two groups and treated with traditional diet and diet formulated with by-products, in order to investigate the action of regulatory elements of the host on its microbiota. The total RNA of the rumen content will be extracted using the Illumina Stranded Total RNA Prep Ligation Kit with Ribo-Zero Plus - 96 reactions. The miRNA data (from ruminal content, and from ruminal epithelium) will be obtained through a project of our research group. With the libraries in hand, use bioinformatics software and approaches, such as RNAhybrid, TargetScan, package R WGCNA and Pearson Correlation, to integrate the miRNA data with the metatranscriptome data. Thus, we will be able, for example, to verify whether the transcripts are targets of miRNAs, as well as to perform co-expression analysis between transcripts from the metatranscriptome and the miRNAs.