Bovine production systems have an important environmental impact due to the production of methane from ruminal microbial fermentation. The generation of enteric methane is known to be associated with animal genetics and the rumen microbiome, it is also negatively associated with feed efficiency in cattle. The importance of viruses in the rumen ecosystem is still poorly understood, although it is recognized that viruses (especially bacteriophages) behave as modulators of the rumen microbiome function together with different mobile genetic elements. Thus, the objective of this project is to identify viral populations and mobile elements associated with methanogenic microorganisms present in samples of Nellore cattle through the Hi-C approach and quantification by real-time PCR of the viruses present in samples of cattle with high and low efficiency feed. Ruminal content samples from 4 Nelore cattle were collected and sent to Phase Genomics to identify viruses and specific mobile elements of microorganisms associated with the methanogenesis process. The microbiome composition of 48 Nellore cattle evaluated for feed efficiency will be estimated by 16s-seq metagenomic analysis performed in our laboratory. A maximum of 5 viruses/microorganism-specific mobile elements associated with the methanogenesis process will be quantified by real-time PCR in samples from animals extreme for the feed efficiency phenotype. These approaches will be essential to characterize the relationships between viruses, mobile elements and their microbial hosts and for future use as microbiome modulators and possible methane mitigation strategy.
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