About Us & Contact

About the Lab

The Comparative Genomics & Metagenomics Laboratory (CGMLab) is led by Jaime Huerta-Cepas at the Centre for Plant Genomics and Biotechnology (CBGP) in Madrid, Spain.

We investigate the diversity, evolution, and functional complexity of microbial communities using comparative genomics, metagenomics, and phylogenomics. Our work spans large-scale analysis of metagenome-assembled genomes (MAGs), reconstruction of microbial phylogenies, and the development of widely-used bioinformatics tools for functional annotation and orthology inference.

A core theme in the lab is understanding microbial diversity at a global scale, including the ecology of the rare biosphere, the functional role of microbiomes in plant-soil systems, and the genomic basis of microbial adaptation and evolution.

Research Areas

Our main research lines include:

• Rare biosphere — Studying low-abundance microbial taxa, their ecology, and evolutionary significance in microbial communities
• Plant microbiome — Metagenomics of plant-associated microbial communities and rhizosphere interactions
• Microbial biodiversity — Comparative genomics and phylogenomics to characterise microbial diversity across Earth's ecosystems
• Functional genomics — Orthology-based functional annotation of microbial genes and metagenomes; development of eggNOG-mapper

Bioinformatics Tools & Resources

We develop and maintain widely-used bioinformatics tools for genomics, metagenomics, and phylogenomics:

• eggNOG-mapper — Ultra-fast functional annotation via orthology assignment; used by thousands of metagenomics studies worldwide
• eggNOG 6.0 — Hierarchical orthology database covering millions of genomes
• ETE Toolkit — Python framework for phylogenetic tree analysis and visualisation
• GeCoViz — Interactive genomic context visualisation for comparative genomics
• PhyloCloud — Cloud platform for large-scale phylogenomic analyses

Location

We are located at the Centre for Plant Genomics and Biotechnology (CBGP), a joint research institute of the Universidad Politécnica de Madrid (UPM) and the Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC).

The CBGP is situated on the Montegancedo UPM campus, in Pozuelo de Alarcón, near Madrid, Spain.