Computational Tool for the Global Analysis of Environmental Metagenome-Assembled Genomes and Isolate Genomes from an ecological perspective

• Grant number: 25/26173-6
• Support Opportunities: Scholarships in Brazil - Doctorate (Direct)
• Start date: December 01, 2025
• End date: November 30, 2030
• Field of knowledge: Biological Sciences - Genetics - Molecular Genetics and Genetics of Microorganisms
• Principal Investigator: João Carlos Setubal
• Grantee: Anderson Cardoso Gonçalves
• 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

With the increasing availability of shotgun-sequenced metagenome datasets, it has become possible to gain an unprecedented understanding of niche-specific microbiomes at a global scale. However, in order to achieve this understanding, new computational tools need to be developed. In this project we will develop one such tool, whose aim is to build a global genome similarity network, and then extract new knowledge from it by mining it from several points of view. The genomes that will be part of this network will be primarily Metagenome-Assembled Genomes, or MAGs, but it will also include isolate genomes. Literature results show that the vast majority (more than 90%) of these genomes are from bacteria; this means that the proposed work has the potential to unlock new knowledge concerning new species of bacteria (represented by MAGs that cannot be classified at the species level) and their ecological properties. At the same time, we propose that the network be made available to the scientific community, and that users will be able to add their own MAGs to the network and ask questions about their MAGs using an especially-developed tool and its graphical interface. This project tackles knowledge gaps pointed out by Wu et al. (2025), who have shown that there are still largely unexplored microbial diversity hotspots in freshwater, marine subsurface, sediment, and soil. (AU)