Integrated analysis of genomic and pangenome diversity of bacterial genera present in metagenomic data

• Grant number: 24/21751-9
• Support Opportunities: Scholarships in Brazil - Scientific Initiation
• Start date: March 01, 2025
• End date: December 31, 2025
• Field of knowledge: Biological Sciences - Biochemistry
• Principal Investigator: João Carlos Setubal
• Grantee: Mariana Louise Gabas
• 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

This project aims to conduct an integrated analysis of the genomic diversity and pangenome of bacterial genera present in the metagenomic dataset from MetaSUB project. For this purpose, we will use the simulated rarefaction curve technique along with the non-parametrics estimators Chao1, Chao2, Jackknife, ICE, and ACE, to estimate the total number of species within the target genera in the MetaSUB dataset. The genera selected for this study are Xanthomonas, Acinetobacter, Stutzerimonas, Stenotrophomonas, and Moraxella. These genera are relatively abundant in the MetaSUB dataset, which was a determining factor for their selection. For each genus, we will compare its rarefaction curve with its pangenome curve, to better understand the relationship between genomic and genetic diversities. Additionally, we will develop scripts to automate most of the analyses; these scripts are going to be a product of this project and can be used to study other target-genera present in the MetaSUB dataset or other metagenomic datasets.