Microbial characterization in a hospital environment using the MinION sequencing platform

• Grant number: 20/14630-0
• Support Opportunities: Scholarships in Brazil - Scientific Initiation
• Start date: December 01, 2020
• End date: November 30, 2021
• Field of knowledge: Biological Sciences - Microbiology - Applied Microbiology
• Principal Investigator: Rafael Silva Rocha
• Grantee: Felipe Marcelo Pereira dos Santos
• Host Institution: Faculdade de Medicina de Ribeirão Preto (FMRP). Universidade de São Paulo (USP). Ribeirão Preto , SP, Brazil
• Associated research grant: 19/15675-0 - Unravelling the complexity of microbial gene regulatory networks, AP.TEM

Abstract

The microbiota, a term that designates the set of microorganisms present in a given environment, has been gaining significant attention regarding its relationship with human health. The most used method for the characterization of microorganisms based on the sequencing results, both in environments such as rivers, water treatment plants or hospitals, and in human mucous membranes, is based on the use of regions of the 16S rRNA gene to carry out their identification. However, such methodology presents an important limitation regarding the identification of species, due to the low variability of the regions used in the 16S rRNA in microorganisms of the same genus and very closely evolutionary species. Although these approaches have good results for the classification of microorganisms according to their phylum and gender, this may not be sufficient for the categorization of pathogens. In order to address this limitation, we begin to use sequencing technologies capable of generating larger sequences, such as MinION, in order to cover the entire 16S rRNA gene and then use it to categorize microorganisms. This approach has already shown more precision regarding the classification of species in relation to the approaches hitherto employed, however, due to the emerging nature of the methodologies, some methods that make up this approach still need to be explored and evaluated. Thus, this project aims to address the limitations of microorganism identification methodologies based on regions of the 16S rRNA gene with the use of this entire gene, sequenced from the MinION sequencing platform.