Genomic sequencing has revolutionized the way we understand biology. Thousands of genomes populate our databases, allowing us to identify what makes each organism unique at the molecular level. It also provide us with an unprecedented power to study the adaptive forces driving the evolution of species, and even inferring their potential interactions with the environment and other organisms.

During the last decade, shotgun sequencing of complete microbial ecosystems (metagenomics) has become possible, revealing unexpected levels of biodiversity and an enormous amount of uncharacterized genetic material.

Our laboratory develops computational methods and genomic resources to characterize microbial communities (microbiomes) from a functional and phylogenetic perspective. We are particularly interested in the characterization of novel functional modules associated with specific environmental conditions. To do so, we combine evolutionary analysis, ecology, massive sequencing data and high performance computational resources.

Our current research lines are:

Comparative metagenomics

We analyze shotgun metagenomics data (soil, ocean, gut, etc.) to identify functional modules within microbial communities that might differentiate sample or environmental conditions. We are particularly interested in exploring the unknown fraction of those data (i.e. sequences with no homologs), currently accounting for 20-50% of the observed unigenes. Our ultimate goals are i) understanding the interactions of microbial communities with their environment, ii) identifying functional modules that can work as markers for specific environmental conditions, and iii) discovering novel gene functions with potential applications in biotechnology (i.e. novel enzymes).

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.

Phylogenomic methods and tools

We develop functional prediction methods, metagenomic frameworks, orthology resources and genomic databases. Many of those tools are the result of our own needs, but we also work on providing open source implementations that are useful to other researchers in the field.