Investigation
At present (2020), our main lines of research are:
Comparative Metagenomics
Our laboratory is interested in the comparative study of microbial communities along different ecosystems (soil, ocean, phyllosphere, animal microbiomes, etc.), in order to identify the functional and phylogenetic traits associated with specific conditions.
We are particularly interested in exploring the unknown fraction of genes observed in such communities - this is, those sequences without homologues in current databases or with a high degree of evolutionary divergence -. Our specific objectives are i) to understand the interactions of microbial communities with their environment, ii) to identify the functional modules that may act as markers of specific environmental conditions, and iii) to discover new gene functions, as well as their possible ecological role and biotechnological applications.
Phylogenetic diversity within microbial communities
Metagenomics data are incomplete, noisy and quite challenging for classic evolutionary analysis. Our goal is to explore and characterize microbial (prok- and eukaryotic) biodiversity using bioinformatic methods. To this end, we work on the implementation and application of phylogenetic methods for taxonomic identification of metagenomic species, the integration of pan-genomic data, and strain resolution.
Evolution at the gene family level
We are interested in different aspects of gene family evolution, such as dating the emergence of specific functions, studying gene duplication, identifying horizontal gene transfers, or characterizing gene fusion events. We are specialized in large scale phylogenomic analysis, where hundreds of genomes can be compared at once. We apply those techniques to gain insights about the evolution of gene function and its relationships with ecological factors.
Phylogenetic methods and tools
We develop bioinformatic methods and tools oriented to functional prediction and metagenomic analysis, as well as web resources and genomic databases. These tools are the result of our own research needs, but we strive to provide open source implementations that are useful to other researchers in the field.