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Sheep rumen metagenome: searching for biomass-degrading bacteria and genes

Grant number: 14/00448-4
Support Opportunities:Scholarships abroad - Research Internship - Doctorate
Effective date (Start): September 01, 2014
Effective date (End): August 31, 2015
Field of knowledge:Agronomical Sciences - Agronomy
Principal Investigator:Rodrigo Mendes
Grantee:Emiliana Manesco Romagnoli
Supervisor: Christopher Dunlap
Host Institution: Escola Superior de Agricultura Luiz de Queiroz (ESALQ). Universidade de São Paulo (USP). Piracicaba , SP, Brazil
Research place: National Center for Agricultural Utilization Research (NCAUR), United States  
Associated to the scholarship:12/24588-4 - Dynamics of the sheep (Ovis aries) rumen microbiome and its relationship with biomass degradation, BP.DR


Currently, the biggest challenge for the industrial production of second-generation biofuels from plant fiber, such as the sugar cane bagasse, is the inefficient degradation of vegetal fiber due to the low activity of hydrolytic enzymes currently available. The discovery of enzymes from microbial communities evolved naturally in biomass degradation, such as from the animal rumen, offers a promising strategy for identification of new lignocellulosic enzymes with better activity. In this context, metagenomics becomes a powerful tool for the discovery of new genomes and active genes involved in biomass degradation. The sheep rumen is a biological system where the biomass degrading microorganisms are naturally enriched which facilitates the directed bioprospection towards to the discovery of new genes and enzymes associated with hydrolysis of vegetal material. Therefore, this project aims to study the microbiome from sheep rumen to discovery new enzymes for biofuel production. To do so, the microbial communities from sheep rumen (Santa Inês breed) will be accessed. These animals will be fed on a basal diet (control) and on a formulated diet for the enrichment of the sugar cane bagasse degrading microorganisms. Two approaches will be used; 1) Sequencing of 16S rDNA gene, aiming the understanding of the bacterial communities structure associated with animals under different diets e for identification groups enriched during biomass degradation; and 2) Sequencing of total DNA, aiming the assessment of the metabolic potential of the rumen microbiome and identification of potential biomass degrading genes. Thus, the ruminal fluid will be sampled over the period of 60 days, and according to the animal performance samples will be selected for library construction (16S rDNA and total DNA) for sequencing. After collecting the ruminal fluid, and followed by DNA isolation and preparation of libraries, it will be used the second-generation sequencer Ion Torrent PGM for generating sequences. The information obtained in this project will open new horizons towards a full understanding of the genomic diversity, functional genes, and metabolic capabilities of the biomass degrading microorganisms, with great prospects to obtain new molecules that may be applied in the biofuel industry. (AU)

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