MDM – Molecular Diversity of Microbes
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MDM projects
Our research revolves around bacteria and their viruses, phages. Facing the abundance and diversity of their viruses, bacteria and archaea have developed multiple lines of defense that can be referred to as « prokaryotic immune systems« . Our research focuses on these anti-phage immune systems. We are trying to understand evolutionary patterns and molecular mechanisms of these systems but also how to use them for medical applications. We work at several scales: from computational genomic analysis on thousands of prokaryotic genomes to experimental molecular genetics and diverse microbiology tools.
Project
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Project
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Project
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Funding
We are very happy to be supported by the following institutions:
- European Research Council (ERC Starting Grant)
- INSERM (ATIP-avenir Grant)
- Bettencourt-Schueller Foundation (CRI fellowship)
- University de Paris Cité (Emergences)
- Region IdF/Marie Curie (CO-fund fellowship)
- Genetics Society of America (Rosalind Franklin Award)
People
Team leader
Aude Bernheim
PhD
Principal Investigator
Bacterial Genetics ; Phage
Biology; Genomics
@AudeBer
aude.bernheim@pasteur.fr
https://mdmlab.fr/
Publications ; CV;
Research Staff
Helena Shomar
Post-doc
Synthetic biology
Metabolic engineering
@HelenaShomar
helena.shomar@inserm.fr
Publications
Matthieu Haudiquet
Post-doc
co-supervised E. Poirier, Institut Curie
Evolutionnary Genomics; Phage biology; Eukaryotic virology
@Matt_Hdqt
matthieu.haudiquet@inserm.fr
Publications
Ernest Mordret
Post-doc
Systems Biology
Data analysis
@howmanyernest1
ernest.mordret@cri-paris.org
Publications
Hugo Vaysset
PhD student
co-supervised P. Hersen, Institut Curie
Data Analysis; Machine Learning
@hugovaysset
hugo.vaysset@cri-paris.org
Jean Cury
Post-doc
Bioinformatics; Evolutionary
biology; Machine Learning
jean.cury@pasteur.fr
Publications
Florian Tesson
PhD student
co-supervised E. Denamur, INSERM IAME
Genomics Anti-phage systems
florian.tesson@cri-paris.org
Heloise Georjon
PhD student
co-supervised V. Libis, Generare Genetics ; Phage biology Streptomyces
heloise.georjon@cri-paris.org
Alumni
2021
Juliette Bernier, Master student (M2)
2022
Margot LeBot, (M1) Paula Thiel Pizarro, (M1) Eduard Sunne, (M2)
Ines Charachon, (M2)
2023
Nicolas Dib, (M2)
Louis Elverston, (M1)
Avishkar Jadhav, (M1)
Publications
2022
- Cury J.*,Mordret E*., Trejo-Hernandez V., Tesson F., Ofir G., Poirier Z. P., Bernheim A.
Conservation of antiviral systems across domains of life reveals novel immune mechanisms in humans
bioRxiv, https://doi.org/10.1101/2022.12.12.520048 (2022) - Tesson F., Hervé A., Touchon M., Mordret E., d’Humières C., Cury J., Bernheim A.
Systematic and quantitative view of the anti-viral arsenal of prokaryotes.
Nature Communications, 13:256 (2022) - Tesson F., Bernheim A.
Synergy and regulation of antiphage systems: toward the existence of a bacterial immune system?.
Curr Opinion in Microbiology, in press - Cury J, Bernheim A
CRISPR-Cas and restriction-modification team up to achieve long-term immunity
Trends in Microbiology S0966-842X(22)00091-9. (2022) - Millman A., Melamed S., Leavitt A., Doron S., Bernheim A, Hör J., Lopatina A., Ofir G., Hochhauser D., Stokar-Avihail A., Tal N., Sharir S., Voichek M., Erez Z., Lorenzo M Ferrer J., Dar D., Kacen A., Amitai G., Sorek R.
An expanding arsenal of immune systems that protect bacteria from phages
Cell Host and Microbes 30, 1556–1569 (2022) - Rousset F., Depardieu F., Miele S., Dowding J., Liebermann E., Garry D., Rocha E.P.C, Bernheim A, Bikard D.
Phages and their satellites encode hotspots of antiviral systems.
Cell Host and Microbes S1931-3128(22)00104-4 (2022) - Klompe S, Jaber N, Bel L, Mohabir J, Bernheim A, Sternberg S.
Evolutionary and mechanistic diversity of Type I-F CRISPR-associated transposons
Molecular Cell 82 (3), 616-628e5 (2022)
2021
- Bernheim A., Millman A., Ofir G., Meitav G., Abraham C., Shomar H., Rosenberg M., Tal N., Melamed S., Amitai G., Sorek R.
Prokaryotic viperins produce diverse antiviral molecules.
Nature, 589, 120-124 (2021)
2020
- Millman A*, Bernheim A*, Stokar-Avihail A.*, Fedorenko T., Voichek M., Leavitt A., Sorek R.
Bacterial retrons function in anti- phage defense
Cell, 183 (6), 1551-1561 (2020) - Bernheim A, Sorek R
The bacterial pan-immune system: anti-phage defense as a community resource
Nature Reviews Microbiology 18, 113–119 (2020) - Bernheim A, Bikard D, Touchon M, Rocha EPC:
Atypical organizations and epistatic interactions of CRISPRs and cas clusters in genomes and their mobile gemetic elements
Nucleic Acids Research 48 (2), 748-760 (2020)
2019
- Bernheim A, Bikard D, Touchon M, Rocha EPC
A matter of background: DNA repair, pathways as a possible cause for the sparse distribution of CRISPR–Cas, systems in bacteria.
Philosophical Transactions of the Royal Society B 374 (1772), 2018008 (2019)
2017
- Bernheim A, Calvo-Villaman A, Basier C, Cui L, Rocha EPC, Touchon M, Bikard D, Inhibition of NHEJ repair by type II-A CRISPR-Cas systems
Nature Communications 8 (1), 1-9 (2017)