Fundings

MicroPENCD - Phylogenetic evolution of human microbiome species to unravel nutrition, cardiometabolic health, and disease relationships

The human microbiome plays a crucial role in health and disease, with specific microbial biomarkers associated with different human conditions. Large-scale computational efforts applying metagenomic assembly have unveiled thousands of previously unknown and prevalent microbial species, many of which were found associated with lifestyle factors and host health. Phylogenomic analyses of these species have expanded our understanding of microbial evolution in the context of the now-expanded microbial diversity. However, current phylogenomic approaches were not designed to scale to this expanded microbial diversity in terms of numbers and genomic information. The MicroPENCD project aims to address these challenges by (i) identifying novel universal phylogenetic markers that accurately model microbial diversity and (ii) developing the next-generation phylogenomic tools for large-scale analyses to integrate reconstructed genomes with partial genomic data. By applying this framework, the project will unveil robust phylogenetic biomarkers for known and unknown microbial species associated with nutrition, cardiometabolic health, and human disease, and further study the evolutionary patterns in these contexts. To this end, MicroPENCD will leverage deep sequencing of human and non-human microbiome data. Findings from these studies will provide insights into microbial evolutionary trajectories and guide future personalized interventions. The developed framework will impact and benefit fields beyond the human microbiome, advancing our abilities in microbial population genomics and epidemiological investigations. Committed to open science, the MicroPENCD project will ensure that generated data, methods, and results are accessible to the research community, promoting collaboration and accessibility. By enabling scalable and accurate microbiome phylogenetic analysis, MicroPENCD will uncover microbial phylogenetic signals, improving our understanding of microbiome evolution and enabling future personalized dietary and biomedical interventions to manage or treat relevant disorders.

Supported by the Ministry of University and Research as part of the FIS 2 initiative - Project Code FIS-2023-03427 - CUP E53C25000400001.