Microbial genomics and evolution
Ph.D., Institute Pasteur, Paris, France
My lab focuses on the evolution of microbial genomes and populations. We apply and develop computational approaches to elucidate the forces that shape the architecture and gene repertoire of microbial genomes. We are particularly interested in understanding the impact of population dynamics on microbial evolution. We are working on the evolution of gene flow across bacterial populations and on the processes leading to microbial speciation.
Evolution of gene repertoires: We have a long-term interest in understanding the processes that drive the evolution of gene repertoires across different lifeforms. This question covers multiple aspects, such as: i) How do new genes originate? ii) What drives gene gain and loss? iii) What causes the disruption of gene flow among microbial populations? iv) What factors determine the diversity of gene repertoires in microbes? We investigate these questions by combining several approaches: Population Genomics, Phylogeny, Comparative Genomics, Metagenomics and Experimental Evolution. We are particularly interested in addressing these questions through large-scale analyses including multiple species living in diverse ecological backgrounds.
Evolution of microbial populations: We are developing a research program addressing the structure of populations within species and the organization of multiple species into their niche. We are applying comparative metagenomic approaches to understand the dynamic of complex microbial populations. Such analyses allow us to precisely follow microbial evolution from individual alleles to entire genotypes. We are particularly interested in understanding the impact of gene flow during the short-term evolution of populations.
Speciation of microbial populations: We study the processes of speciation in microbes. This project seeks to understand the mechanisms that lead to speciation in non-sexual organisms. In particular, we are comparing the speciation process in clonal and recombining microbes. We are focusing on the mechanisms that drive genotype divergence or convergence of microbial populations and the impact of gene flow.
Bobay LM, Raymann K. Population genetics of host-associated microbiomes. Curr Mol Biol Rep. 2019. In press. doi: 10.1007/s40610-019-00122-y.
Bobay LM, Ochman H. Factors driving effective population size and pan-genome evolution in bacteria. BMC Evol Biol. 2018; 18:153. doi: 10.1186/s12862-018-1272-4.
Bobay LM, Ochman H. Biological species in the viral world. Proc Natl Acad Sci U S A. 2018. 115:6040-6045. doi: 10.1073/pnas.1717593115.
Bobay LM, Ellis BS, Ochman H. ConSpeciFix: Classifying prokaryotic species based on gene flow. Bioinformatics. 2018. 34; 3738-3740. doi: 10.1093/bioinformatics/bty400.
Raymann K*, Bobay LM*, Moran NA. Antibiotics reduce genetic diversity of core species in the honeybee gut microbiome. Mol Ecol. 2017; 27:2057-2066. doi: 10.1111/mec.14434.
* these authors contributed equally to this work.
Bobay LM, Ochman H. Impact of recombination on the base composition of Bacteria and Archaea. Mol Biol Evol. 2017. doi: https://doi.org/10.1093/molbev/msx189
Bobay LM, Ochman H. The evolution of bacterial genome architecture. Front Genet. 2017; 8:72. doi: 10.3389/fgene.2017.00072
Bobay LM, Ochman H. Biological species are universal across life’s domains. Genome Biol Evol. 2017. doi: 10.1093/gbe/evx026.
Wexler AG, Bao Y, Whitney JC, Bobay LM, Xavier JB, Schofield WB, Barry NA, Russell AB, Tran BQ, Goo YA, Goodlett DR, Ochman H, Mougous JD, Goodman AL. Human symbionts inject and neutralize antibacterial toxins to persist in the gut. Proc Natl Acad Sci U S A. 2016; 113:3639-44.
Bobay LM, Traverse CC, Ochman H. Impermanence of bacterial clones. Proc Natl Acad Sci U S A. 2015; 112:8893-900.
Douam F*, Bobay LM*, Maurin G, Fresquet J, Cosset FL, Féray C, Lavillette D. Strong specialization of HCV envelope glycoproteins is associated with the establishment of B-lymphocyte reservoirs in chronically infected patients. J Virol. 2015; 90:992-1008. * these authors contributed equally to this work.
Henry M, Bobay LM, Chevallereau A, Saussereau E, Ceyssens PJ, Debarbieux L. The search for therapeutic bacteriophages uncovers one new subfamily and two new genera of Pseudomonas-infecting Myoviridae. PLoS One. 2015; 10:e0117163.
Bobay LM, Touchon M, Rocha EP. Pervasive domestication of defective prophages by bacteria. Proc Natl Acad Sci U S A. 2014; 111:12127-32.
Touchon M, Bobay LM, Rocha EP. The chromosomal accomodation and domestication of mobile genetic elements. Curr Opin Microbiol. 2014; 22:22-9.
Bobay LM, Touchon M, Rocha EP. Manipulating or superseding host recombination functions: a dilemma that shapes phage evolvability. PLoS Genet. 2013; 9:e1003825.
Bobay LM, Rocha EP, Touchon M. The adaptation of temperate bacteriophages to their host genomes. Mol Biol Evol. 2012; 30:737-751.
Raymann K, Bobay LM, Doak TG, Lynch M, Gribaldo S. A genomic survey of reb homologs suggests widespread occurrence of R-bodies in Proteobacteria. G3 (Bethesda). 2013; 3:505-16.
Deghorain M, Bobay LM, Smeesters PR, Bousbata S, Vermeersch M, Perez-Morga D, Drèze PA, Rocha EP, Touchon M, Van Melderen L. Characterization of novel phages isolated in coagulase-negative staphylococci reveals evolutionary relationships with Staphylococcus aureus phages. J Bacteriol. 2012; 194:5829-39.
Lynch M, Bobay LM, Catania F, Gout JF, Rho M. The repatterning of eukaryotic genomes by random genetic drift. Annu Rev Genomics Hum Genet. 2011; 12:347-66.