Tuesday, April 9, 2024

Welcome to the Comparative Genomics & Metagenomics Lab

We study the diversity and biological complexity of microbial communities (microbiome) through genomic sequencing and computational techniques.

Latest News & Papers

Functional and evolutionary significance of unknown genes from uncultivated taxa

Many of the Earth’s microbes remain uncultured and understudied, limiting our understanding of the functional and evolutionary aspects of their genetic material, which remain...

Research Lines

We investigate the ecological and functional role of low-abundance microorganisms across different habitats.

We study soil, rhizosphere, and phyllosphere microbiota in various crops in order to model plant-microbe interactions and stress resistance.

We use phylogenomics to study microbial biodiversity and ecological patterns at a planetary scale.

We develop tools, methods, and databases that facilitate large-scale functional and evolutionary comparisons among genes, genomes, and metagenomes.

Latest Scientific Papers

Functional and evolutionary significance of unknown genes from uncultivated taxa

Many of the Earth’s microbes remain uncultured and understudied, limiting our understanding of the functional and evolutionary aspects of their genetic material, which remain...

GeCoViz: genomic context visualisation of prokaryotic genes from a functional and evolutionary perspective

GeCoViz is an online resource providing fast and interactive visualisation of genomic context conservation of prokaryotic genes grouped by orthologous group or PFAM domains.

PhyloCloud: an online platform for making sense of phylogenomic data

PhyloCloud is an online platform aimed at hosting, organizing, sharing, exploring and analyzing trees and alignments from their phylogenomics projects.

eggNOG 6.0: enabling comparative genomics across 12 535 organisms 

The eggNOG (evolutionary gene genealogy Non-supervised Orthologous Groups) database is a bioinformatics resource providing orthology data and comprehensive functional information for organisms from all...

Towards the biogeography of prokaryotic genes

Microbial genes encode the majority of the functional repertoire of life on earth. However, despite increasing efforts in metagenomic sequencing of various habitats1,2,3, little...

Prevalence and Specificity of Chemoreceptor Profiles in Plant-Associated Bacteria

Considering the enormous variety of LBDs at sensor proteins, an important question resides in establishing the forces that have driven their evolution and selection. We present here the first clear demonstration that environmental factors play an important role in the selection and evolution of LBDs. We were able to demonstrate the existence of LBD families that are highly enriched in plant-associated bacteria but show a wide phylogenetic spread. These findings offer a number of research opportunities in the field of single transduction, such as the exploration of similar relationships in chemoreceptors of bacteria with a different lifestyle, like those inhabiting or infecting the human intestine.

Our tools and resources

ETE Toolkit
A python package for analysis and visualization of phylogenomic data

eggNOG Database
A database of orthology relationships, functional annotation, and gene evolutionary histories.

eggNOG-mapper
A tool for functional annotation, orthology assignments, and domain prediction at the metagenomic scale

PhyloCloud
An online platform for making sense of sharing and visualasing phylogenomic data

GeCoViz
Online Genomic Context Visualizer

Where to find us