The Microbial Evolutionary Genomics five-years group is devoted to the study of prokaryotic evolution by means of computational and statistical analysis of biological data, most notably genome and protein sequences. Our work is at the crossroads of microbiology, molecular genetics, evolutionary ecology and population genetics. Our work aims at answering the following questions: 1) How and why are bacterial genomes organised. 2) How dynamic are genomes? 3) What results from the trade-off between organisation and dynamics? 4) What are the implications of genome dynamics in ecological terms?

Our studies have shown that replication and growth have an outstanding impact on long-scale genome organization in prokaryotes. Genome size and coding density are not correlated with minimum generation time, highlighting the mechanistic uncoupling of bacterial division with chromosome replication. Our latest studies highlighted three highly correlated types of traits associated with fast growth: i) stable amplification of rRNA and tRNA genes, ii) localization of highly expressed genes (HEG) near the origin of replication, iii) use of optimal codons in HEG. Genomes organized for fast growth tend to be more stable, i.e.to accumulate genomic rearrangements at a slower pace than average. The statistical modelling of growth-related trends of genome organization allowed us to create a predictor of minimal generation time (Figure 1), which we used to study metagenomes.With this, we found evidence for the classical island biogeography prediction that colonizers grow faster than elements of stable communities in the human gut colonization after birth (Figure 1). This method pioneers the use of metagenomics to study the evolutionary ecology and physiology of growth.

Keywords: Molecular evolution, bioinformatics, bacterial genomics

1. Vieira-Silva S, Rocha EPC (2010) The Systemic Imprint of Growth Rates and its Uses in Ecological (Meta)genomics. Plos Genetics 6 : e1000808.

2. Smillie C, Garcillán-Barcia MP, Francia MV, Rocha EPC*, de la Cruz F* (2010) The mobility of plasmids. Microbiol Mol Biol Rev. 74:434-52.

3. Nogueira T, Rankin DJ, Touchon M, Taddei F, Brown SP, Rocha EPC (2009) Horizontal gene transfer of the secretome drives the evolution of bacterial cooperation and virulence. Current Biology 19:1683-91.

4. Touchon M, ... (+37 co-authors) ... Rocha EPC, Denamur E (2009) Organised genome dynamics in the Escherichia coli species: the path to adaptation. Plos Genetics 5:e1000344.

5. Rocha EPC (2008) The organization of the bacterial genome. Annu Rev Genetics 42:211-33.