Development and application of a computational tool for surveys of bacterial species using metagenomics datasets

• Grant number: 24/01729-9
• Support Opportunities: Scholarships in Brazil - Doctorate (Direct)
• Start date: November 01, 2024
• End date: October 31, 2029
• Field of knowledge: Biological Sciences - Microbiology
• Principal Investigator: João Carlos Setubal
• Grantee: Arthur Henrique Barrios Solano
• Host Institution: Instituto de Química (IQ). Universidade de São Paulo (USP). São Paulo , SP, Brazil
• Associated research grant: 21/10577-0 - Biology of Bacteria and Bacteriophages Research Center, AP.CEPID

Abstract

We propose to develop a computational pipeline that will allow us to carry out a global diversity survey of bacterial genera of interest, using metagenomics datasets. We have pre-selected four genera: Xanthomonas, Acinetobacter, Moraxella, Stutzerimonas, and Stenotrophomonas. The criteria for this selection were primarily their occurrence in the MetaSUB dataset and interest on the part of CEPID B3 researchers; other genera may be added to the project as it makes progress. As part of this project we intend not only to survey known species but also to identify novel species. The pipeline to be developed will be made publicly available, so that other researchers will be able to use it for their own genera of interest. Preliminary results show that our methodology is more accurate than generic tools for taxonomic identification of metagenome fragments, which allowed us to identify several known species of Xanthomonas and Acinetobacter in the MetaSUB dataset, as well as a few potential novel species in these genera.