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 MoreTreeProfiler 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.
What uncultivated, low-abundance microbes do and how they evolve.
We develop metagenomic and phylogenetic approaches to probe the vast pool of uncultivated, low-abundance organisms — the rare biosphere — and their unknown genes. We ask what these hidden taxa contribute, how their communities shift under environmental change, and why so much microbial diversity remains functionally dark.
High-resolution metagenomics to monitor biodiversity across ecosystems and hosts.
We build targeted and shotgun metagenomic technologies to catalogue microbial biodiversity and track community dynamics — from soils and crops to the human microbiome. Our work links taxonomic and functional profiling to real environmental and biomedical questions, from agricultural sustainability to microbiome-driven health.
Assigning function and evolutionary history to genes across the tree of life.
We infer gene function and evolution at scale through orthology, pangenomics and comparative genomics. Flagship resources such as eggNOG deliver phylogeny-based orthology and functional annotation across tens of thousands of organisms, underpinning how the community annotates newly sequenced genomes and metagenomes.
Open software to analyse and visualise data at the scale of the tree of life.
We create widely used open-source tools for large-scale phylogenomics and comparative analysis — including the ETE Toolkit, TreeProfiler, PhyloCloud and GeCoViz — and contribute to bioinformatics infrastructure (ELIXIR). Our focus is making massive genomic and tree data tractable, reproducible and easy to explore.
Mining microbial diversity for enzymes, antimicrobials and industrial ingredients.
We turn microbial genomic diversity into useful molecules, combining metagenomics, machine learning and computational modelling to discover novel enzymes, antimicrobial peptides and natural ingredients. Projects like ORIGIN translate microbial dark matter into sustainable industrial and biomedical applications.
How crop-associated microbes shape plant health under stress.
We study the functional and community dynamics of plant-associated microbiota, focusing on low-abundance organisms and how plant–microbe interactions respond to heat, nutrient scarcity and changing crop conditions. The goal is to harness the microbiome for more resilient, sustainable agriculture.
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 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 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
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
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
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).
We are based at the Centre for Plant Genomics and Biotechnology (CBGP), a joint (UPM-INIA/CSIC) research institute in Madrid (Spain).
