Research / Microbial Phylogenomics

Microbial Phylogenomics - Simonetta Gribaldo


Our research focuses on the evolutionary history of microbes at various nodes of the Tree of Life through phylogenomics approaches.

We are particularly interested in large-scale microbial phylogeny, and in the emergence and evolution of key cellular structures and processes (phylogenomics of microbial systems), with a focus on the evolutionary links among the three domains of life (Archaea, Bacteria, Eucarya).

We are here :
Institut Pasteur, 25 rue Docteur Roux, 75015 PARIS


Simonetta Gribaldo (Principal Investigator)  

        Simonetta obtained her PhD at the University “La Sapienza” of Rome (Italy) in 2001 with a thesis in molecular phylogeny on issues related to ancient evolution and the Tree of Life.

She arrived in France in 2001 as a post-doc in the group of Hervé Philippe at the University Paris 6, where she worked on the evolution of duplicated gene families.

In 2003 she joined the group of Patrick Forterre at the University Paris-Sud, where she started working on the phylogeny of Archaea.

In 2005 she obtained a permanent position at the Institut Pasteur, Paris, in the newly formed Unit Biologie Moleculaire du Gene chez les Extremophiles, where she runs the “Microbial Phylogenomics” group.

 Current members :

Kasie Raymann (PhD student)

Kasie obtained a grant from the Pasteur - Paris University International Doctoral Program (

Malvina Kadlec (Master student)

Bonora Mario Neou (Master student, together with the Unit Biologie des Bactéries intracellulaires, Department of Génomes et Génétique)

Past members:

Alexis Criscuolo (Post-doc -2008/2010)

Alexis worked on the large-scale phylogeny of Cyanobacteria and on the origin of primary plastids (PhyloCyano project funded by ANR), as well as methodology development.
He is currently post-doc at the Pasteur Institute, Plateforme de génotypage des pathogènes et santé publique (PF8)

Elie Desmond (PhD -2007/2010)

Elie worked on the phylogenomic analysis of different eukaryotic systems in order to understand the early evolution of Eukaryotes and their link with Bacteria and Archaea.
He is currently post-Doc at CEMAGREF, France.

Diego Cortez (PhD -2006/2010)

Diego worked on the bioinformatics detection of integrative elements in prokaryotic genomes and on the identification of the terminus of replication in archaea.
He is currently post-Doc at Centre Integrative Genomique, Lausanne, Switzerland.

Céline Petitjean (Master student -2009)

Céline worked on the evolutionary link between Thaumarchaeota and Eukaryotes, and on the phylogenomic analysis of different archaeal systems.
She is currently doing her PhD thesis under the supervision of Céline Brochier-Armanet at the University of Lyon, and David Moreira at the University Paris-Sud.




Criscuolo A and Gribaldo S (2010) BMGE (Block Mapping and Gathering with Entropy): a New Software for   Selection of Phylogenetic Informative Regions from Multiple Sequence Alignments. BMC Evol Biol 13;10:210.


Criscuolo A. (2011) morePhyML: improving the phylogenetic tree space exploration with PhyML 3. Mol Phylogenet Evol. 61(3):944-8.


Positions are regularly available in our group.

We search highly motivated Master, PhD students and Post-docs with good informatics skills, previous experience with comparative genomics and/or molecular phylogenetics and a strong interest in evolution.

Please send an email with a brief statement of your interests and a CV to


Some publications of the group:  

Brochier-Armanet C, Gribaldo S, Forterre P. Evolution: Spotlight on the Thaumarchaeota. (2011) ISME J. Nov 10. [Epub ahead of print]

Criscuolo A and Gribaldo S (2011) Large-scale phylogenomic analyses indicate a deep origin of primary plastids within Cyanobacteria. Mol Biol Evol 28(11):3019-32

Brochier-Armanet C, Forterre P, Gribaldo S (2011) Phylogeny and evolution of the Archaea: one hundred genomes later. Curr Opin Microbiol 14(3):274-81.

Gribaldo S, Forterre P, Brochier-Armanet C. Editorial : Archaea and the tree of life. (2011) Res Microbiol 162(1):1-4

Desmond E, Brochier-Armanet C, Forterre P, and Gribaldo S (2011) On the last eukaryotic common ancestor and early eukaryotic evolution: reconstructing the history of mitochondrial ribosomes. Res Microbiol 162(1):53-70.

Gribaldo S, Poole AM, Daubin V, Forterre P, Brochier-Armanet C (2010) The origin of eukaryotes and their relationship with the Archaea: are we at a phylogenomic impasse? Nat Rev Microbiol  8(10):743-52.

Cortez D, Quevillon-Cheruel S, Gribaldo S, Desnoues N, Sezonov G, Forterre P, Serre MC. (2010) Evidence for a Xer/dif system for chromosome resolution in Archaea. PLoS Genetics 6(10):e1001166.

Criscuolo A and Gribaldo S (2010) BMGE (Block Mapping and Gathering with Entropy): a New Software for Selection of Phylogenetic Informative Regions from Multiple Sequence Alignments. BMC Evol Biol 13;10:210.

Desmond E and Gribaldo S (2009) Phylogenomics of sterol synthesis: insights into the origin, evolution and diversity of a key eukaryotic feature. Genome Biol Evol 2009:364-81.

Gribaldo S, Talla E, Brochier-Armanet C. (2009) Evolution of the haem copper oxidases superfamily: a rooting tale. Trends Biochem Sci 34(8):375-81.

Gribaldo S, Brochier C. (2009) Phylogeny of prokaryotes: does it exist and why should we care? Res Microbiol 160 (7) :513-21.

Cortez D, Forterre P, Gribaldo S. (2009) A hidden reservoir of integrative elements is the major source of recently acquired foreign genes and ORFans in archaeal and bacterial genomes. Genome Biology 10(6):R65.

Emiliani G, Fondi M, Fani R, Gribaldo S (2009) A horizontal gene transfer at the origin of phenylpropanoid metabolism: a key adaptation of plants to land. Biology Direct 16;4(1):7.

Brochier-Armanet C, Gribaldo S, and Forterre P (2008) A DNA Topoisomerase IB in Thaumarchaeota testifies for the presence of this enzyme in the last common ancestor of Archaea and Eucarya. Biology Direct 3:54.

Brochier-Armanet C, Talla E, Gribaldo S (2008) The multiple evolutionary histories of dioxygen reductases: implications for the origin and evolution of aerobic respiration. Mol Biol Evol 26(2):285-97

Brochier-Armanet C, Boussau B, Gribaldo S, Forterre P. (2008) Mesophilic Crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota. Nat Rev Microbiol 6(3):245-52.

Desmond E, Brochier-Armanet C, Gribaldo S (2007) Phylogenomics of the archaeal flagellum: rare horizontal gene transfer in a unique motility structure. BMC Evol Biol 2;7:106.

Forterre P and Gribaldo S (2007) The origin of modern terrestrial life. Human Frontiers Science Program Journal 1; 3:156-168. Review.

Forterre P, Gribaldo S, Gadelle D, Serre MC (2007) Origin and evolution of DNA topoisomerases. Biochimie 89(4):427-46. Review.

Gribaldo S and Brochier C (2006) The origin and evolution of the Archaea : a state of the art. Proc Royal Acad Sci 361(1470):1007-22. Review.

Brochier C, Gribaldo S, Forterre P (2005) An emerging phylogenetic core of Archaea: phylogenies of transcription and translation machineries converge following addition of new genome sequences. BMC Evol Biol 5(1):36.

Brochier C, Gribaldo S, Zivanovic Y, Confalonieri F, Forterre P (2005) Nanoarchaea: representatives of a novel archaeal phylum or a fast-evolving euryarchaeal lineage related to Thermococcales? Genome Biology 6(5):R42.


Science vulgarization (in French):

Brochier-Armanet C, Gribaldo S Les defies de la systématique face au monde microbien. Biofutur (Janvier 2012) 328: 49-52.

Gribaldo S, Forterre P, Brochier-Armanet C (2008) Les Archaea, évolution et diversité du troisième domaine du vivant. Bulletin de La Société Française de Microbiologie 23(3): 137-145.

Gribaldo S, Maurel MC, Vannier J (2007) Les Débuts de la vie. Editions Le Pommier.

Forterre P, Gribaldo S, Brochier C (2005) Luca: the last universal common ancestor Med Sci (Paris) 21(10):860-5.