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Development of protocols and large-scale strategies to identify microorganisms

Abstract

Next generation sequencing (NGS) methodologies are able to sequence thousands of fragments and generate information on millions of bases in a single run. These methods have revolutionized research in genomics, transcriptomics and metagenomics. Compared to the classic Sanger method, NGS has substantially greater performance and run time as well as lower price per base sequenced (Behjati1 & Tarpey, 2013). In microbiology, NGS has replaced traditional culture-based techniques to characterize microorganisms. Genome studies of microbiotas found in a given habitat is known as metagenomics (Von Mering et al., 2007). Metagenomics has provided information on the composition, diversity, structure and metabolic potential of microbial communities, including non-cultivable microorganisms directly recovered from samples of the environment (Streit & Schmitz, 2004, Tringe & Rubin, 2005, Teeling & Glöckner, 2012), digestive tract of humans, pigs, poultry and ruminants (Ferguson et al., 2016, Kim & Mundt, 2011, Hendersen et al., 2015), milk (Oikonomou et al., 2012), soil (Daniel, 2005 ) and products of industrial fermentation (Hong et al., 2016).In agriculture, metagenomics can help in the great challenge of producing food without the use of antibiotics. Subtherapeutic doses of antibiotics act as growth promoters by favorably modulating the population of microorganisms in the digestive tract of animals that are involved in absorbing nutrients and improving the immune system (Choi et al., 2015) or by inhibiting bacteria growth in fermentation vats (Amorin et al., 2011). However, concern about developing resistant strains is leading to a ban on antibiotic use, which has stimulated the creation of new technologies to model microorganism populations (Schmieder & Edwards, 2012). As a result, many companies dedicated to the development of prebiotics, probiotics and plant extracts to modify the microbiome and reduce antibiotic use have emerged. The number of articles using NGS for microbial diversity studies has doubled every year since 2010 (Web of Science). However, commercial application in environmental and agricultural areas is still restricted, probably due to the cost of analysis. A brief market research in Brazil revealed that the cost of 16S rRNA sequencing using NGS ranged from R$208 to R$600 per sample. Even considering that the cost per base sequenced has dramatically declined over the last few years, the value per sample is still high for large-scale applications. In the present project, NGS Soluções Genômicas will demonstrate the feasibility of developing low cost NGS strategies for environmental and agricultural areas. NGS Soluções Genômicas is a technology-based company associated with the business incubator of the Luiz de Queiroz College of Agriculture (ESALQTec) that is dedicated to the development of genomic technologies as well as research and analysis of sequence data. To carry out this proposal, the company will rely on the cooperation of a team of researchers and specialized laboratories at ESALQ-USP. (AU)

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