Eduardo Rocha

Website: https://research.pasteur.fr/en/team/microbial-evolutionary-genomics/
ORCID: 0000-0001-7704-822X
Twitter: @epcrocha

The Microbial Evolutionary Genomics Unit is composed of researchers from different backgrounds including microbiologists, evolutionary biologists, geneticists, bioinformaticians, and computer scientists. It has a large experience on the use of comparative genomics and population genetics approaches to study microbial evolution. While most of its research is hypothesis driven and centered on biological questions, it also develops extensive work in the production of novel software for the analysis of bacterial genomes.

Our laboratory aims at identifying natural variants in bacterial populations, understand the mechanisms driving the emergence of these variants, and discover their adaptive effects. For this, it is necessary to study the mechanisms of horizontal transfer, their constraints and how they result in the integration of new functions in cellular systems.

The lab’s work is structured around five major questions:
-How can genomes be organized while having high rates of horizontal gene transfer?
-What are the key gene transfer mechanisms (and their determinants)?
-How does the cell modulate the rates of transfer?
-How do the new functions fit into the biology of the cell?
-What remains of mobile genetic elements and other acquired genes in the long term?

For this we use different types of approaches: bioinformatics; comparative genomics; phylogenomics; modelling; molecular genetics; evolution experiments. We study many adaptive traits, including antibiotic resistance, virulence, and mutualism, and cellular components, such as the bacterial capsule, secretion systems, defense systems, etc.

The lab has standard technology for experimental microbiology. We have developed software to identify secretion systems, capsules, defense systems, conjugation systems, integrons, etc. We have also developed fully automated pipelines for large scale comparative genomics.

Top 5 publications

1. Haudiquet M, Buffet A, Rendueles O*, Rocha EPC* (2021) Interplay between the cell envelope and mobile genetic elements shapes gene flow in populations of a nosocomial pathogen. PLoS Biology 19(7): e3001276 https://doi.org/10.1371/journal.pbio.3001276

2. Sousa JAM, Pfeifer E, Touchon M, Rocha EPC (2021) Causes and consequences of bacteriophage diversification via genetic exchanges across lifestyles and bacterial taxa. Mol Biol Evol 38:2497-2512. 10.1093/molbev/msab044

3. Pfeifer E, Sousa JAM, Touchon M, Rocha EPC (2021) Bacteria have numerous well-related and highly-diverse groups of phage-plasmids with conserved phage and variable plasmid gene repertoires. Nucleic Acids Res 49: 2655-2673. https://doi.org/10.1093/nar/gkab064

4. Touchon M, Perrin A, de Sousa JAM, Vangchhia B, Burn S, O’Brien CL, Denamur E, Gordon D, Rocha EPC (2020) Phylogenetic background and habitat drive the genetic diversification of Escherichia coli. PLoS Genetics 16(6):e1008866. https://doi.org/10.1371/journal.pgen.1008866

5. Denise R, Abby SS*, Rocha EPC* (2019) Diversification of the type IV filament superfamily into machines for adhesion, protein secretion, DNA uptake, and motility. PLoS Biology 17:e3000390. doi: 10.1371/journal.pbio.3000390.

Dernières publications sur HAL :