Development of customized genomic solutions for agribusiness based on next generation sequencing (NGS) and bioinformatics strategies for characterization of microbiomes

Abstract

The progress of next generation sequencing technologies (NGS), in line with the drastic reduction of sequencing costs, has revolutionized human medicine and can add value to agribusiness. New sequencing technologies allow the study of complex biological samples, enabling the taxonomic and functional characterization of microbial communities that practically colonize all ecological niches. Molecular identification of microorganisms should replace conventional characterization, based on clonal cultures, providing a more accurate, sensitive and less laborious genomic definition. This new methodology can be applied in the identification of contaminating, deteriorating and / or pathogenic microorganisms found in beverages and foods and in industrial alcoholic fermentation products, which hinder the process yield and the quality of the final product. In agriculture, the characterization of the microbiome present in the gastrointestinal tract (GIT) may help in the great challenge of producing food without the use of antibiotics. The microbiota plays a central role in enhancing nutrient absorption and strengthening the immune system, affecting both growth and animal health. This project aims to develop researches with the potential to generate commercial DNA sequencing technologies customized for the identification of microorganisms in different areas of agribusiness. The customization of these methodologies for different applications is determinant for the commercial success of this technology. It is necessary to determine which region of DNA is to be sequenced to maximize the identification of microorganisms of interest for each application, since distinct regions show considerable differences in taxonomic coverage. Furthermore, the development of specific databases for different microbiomes is essential to optimize the resolution power of the taxonomic classification of microorganisms and to monitor microorganisms of interest to the end user of the technology. In phase 1 of this PIPE project, NGS GENOMIC SOLUTIONS demonstrated the feasibility of applications of lower cost NGS strategies applied to agribusiness and established partnerships for the future development and commercialization of this technology with leading companies in Agribusiness in Brazil. Considering the partnerships developed, the present project aims to address the specific needs of dairy farms and industries, broiler chicken and industrial alcoholic fermentation. (AU)