Welcome to the Comparative Genomics & Metagenomics Lab
We study microbial diversity, microbiome ecology, and evolution using comparative genomics, metagenomics, and phylogenomics. Our work spans the rare biosphere, plant microbiome, functional genomics, and the development of open bioinformatics tools.
Learn MoreHighlights
TreeProfiler: large-scale metadata profiling along gene and species trees.
TreeProfiler is a command-line tool that annotates any phylogenetic tree with metadata (ecology, taxonomy, phenotypes) and lets researchers visualise and query patterns across thousands of tips at once.
deluxpore: a Nextflow pipeline for demultiplexing Illumina dual-indexed Nanopore libraries
Research Lines
Studying low-abundance microbial taxa and their roles in ecosystem function and evolution.
Investigating the microbiomes associated with plants and their interactions in the rhizosphere.
Characterizing the full extent of microbial diversity across Earth's habitats and ecosystems.
Unraveling the functions of microbial genes and proteins across diverse genomic contexts.
Latest Scientific Papers
deluxpore: a Nextflow pipeline for demultiplexing Illumina dual-indexed Nanopore libraries
demultiplexing and basecalling pipeline for Nanopore sequencing runs with dual-indexed Illumina-style barcodes, packaged as a reproducible Nextflow workflow.
doi:10.64898/2026.03.27.714410 bioRxiv (2026).
TreeProfiler: large-scale metadata profiling along gene and species trees.
TreeProfiler is a command-line tool that annotates any phylogenetic tree with metadata (ecology, taxonomy, phenotypes) and lets researchers visualise and query patterns across thousands of tips at once.
43(2):msag028, 2026
eggNOG v7: phylogeny-based orthology predictions and functional annotations.
eggNOG v7 expands the gold-standard database of orthologous genes to cover 12,000+ species, adding phylogeny-aware functional predictions that help scientists interpret what newly sequenced genes do.
54(D1):D402-D408, 2026
Root growth promotion by Penicillium melinii: mechanistic insights and agricultural applications.
The soil fungus Penicillium melinii boosts root growth in crops by producing specific metabolites; the study maps the molecular mechanisms behind this plant-growth promotion.
2025.12.05.692050, 2025
The Biodiversity Cell Atlas: mapping the tree of life at cellular resolution.
A global atlas mapping gene expression across the full tree of life at the single-cell level, revealing universal and lineage-specific cell-type programmes from microbes to animals.
645(8082):877-885, 2025
Unveiling the hidden biodiversity of microbial chemoreceptor genes in the rare biosphere
A deep dive into environmental DNA databases reveals that chemoreceptor genes—bacterial sensors for chemical signals—are far more diverse and widespread in rare microbial communities than previously thought.
doi:10.1101/2025.06.24.661292 bioRxiv (2025).
Our Tools & Resources
Where to Find Us
We are based at the Centre for Plant Genomics and Biotechnology (CBGP), a joint (UPM-INIA/CSIC) research institute in Madrid (Spain).
