Molecular Diversity of Microbes Lab

Selected publications

Predicting phage-bacteria interactions at the strain level from genomes
Gaborieau B*, Vaysset H*., Tesson H*., Charachon I., Dib N., Bernier J., Dequidt T., Georjon H., Clermont O., Hersen P., Debarbieux L, Ricard JD, Denamur E., Bernheim A
bioRxiv, 2023.11. 22.567924 (2023)

Viperin immunity evolved across the tree of life through serial innovations on a conserved scaffold
Shomar H*.,Georjon H.*, Feng Y, Olympio B, Cury J, Tesson F., Wu F*., Bernheim A*.
bioRxiv https://www.biorxiv.org/content/10.1101/2023.09.13.557418v1

The highly diverse antiphage defence systems of bacteria
Georjon H, Bernheim A.
Nature Reviews Microbiology, 1/-15 (2023)

Conservation of antiviral systems across domains of life reveals novel immune mechanisms in humans
Cury J.*,Mordret E*., Trejo-Hernandez V., Tesson F., Ofir G., Poirier Z. P., Bernheim A.
bioRxiv, https://doi.org/10.1101/2022.12.12.520048 (2022)

Systematic and quantitative view of the anti-viral arsenal of prokaryotes
Tesson F., Hervé A., Touchon M., Mordret E., d’Humières C., Cury J., Bernheim A.
Nature Communications, 13:256 (2022)

Prokaryotic viperins produce diverse antiviral molecules
Bernheim A., Millman A., Ofir G., Meitav G., Abraham C., Shomar H., Rosenberg M., Tal N., Melamed S., Amitai G., Sorek R.
Nature, 589, 120-124 (2021)

All publications

2024

A Comprehensive Resource for Exploring Antiphage Defense: DefenseFinder Webservice, Wiki and Databases.
Tesson F., Planel R., Egorov A., Georjon H., Vaysset H., Brancotte B., Neron B., Mordret E., Atkinson G., Bernheim A*, Cury J*
bioRxiv, 2024.01. 25.577194

Viral proteins activate PARIS-mediated tRNA degradation and viral tRNAs rescue infection
Burman N.*, Belukhina S.* , Depardieu F.*, Wilkinson R.*, Skutel M., Santiago-Frangos A., Graham A., Livenskyi A., Chechenina A., Morozova N, Zahl T., Henriques W., Buyukyoruk M., Rouillon C., Shyrokova L, Kurata, T Hauryliuk V, Severinov K, Groseille J, Thierry A, Koszul R., Tesson F., Bernheim A, Bikard D., Wiedenheft B, Isaev A.
bioRxiv, 2024.01. 02.573894

Lessons from twenty years of the life of commensal Escherichia coli populations in a human gut
Condamine B, Morel-Journel T., Tesson F., Magnan M., Bernheim A., Denamur E., Blanquart F. , Clermont O.
bioRxiv, 2024.02. 21.581337

2023

The highly diverse antiphage defence systems of bacteria
Georjon H, Bernheim A.
Nature Reviews Microbiology, 1/-15 (2023)

Genomic characterization of the antiviral arsenal of Actinobacteria
Georjon H., Tesson F., Shomar H*., Bernheim A*.
Microbiology Aug;169(8):001374 (2023)

Synergy and regulation of antiphage systems: toward the existence of a bacterial immune system?
Tesson F., Bernheim A.
Curr Opinion in Microbiology Feb:71:102238 (2023)

Immunité bactérienne: à la découverte d’un nouveau monde
A Hardy, H Shomar, A Bernheim
médecine/sciences 39 (11), 862-868

2022

Conservation of antiviral systems across domains of life reveals novel immune mechanisms in humans
Cury J.*,Mordret E*., Trejo-Hernandez V., Tesson F., Ofir G., Poirier Z. P., Bernheim A.
bioRxiv, https://doi.org/10.1101/2022.12.12.520048 (2022)

Systematic and quantitative view of the anti-viral arsenal of prokaryotes
Tesson F., Hervé A., Touchon M., Mordret E., d’Humières C., Cury J., Bernheim A.
Nature Communications, 13:256 (2022)

CRISPR-Cas and restriction-modification team up to achieve long-term immunity
Cury J, Bernheim A
Trends in Microbiology S0966-842X(22)00091-9. (2022)

An expanding arsenal of immune systems that protect bacteria from phages
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.
Cell Host and Microbes 30, 1556–1569 (2022)

Phages and their satellites encode hotspots of antiviral systems
Rousset F., Depardieu F., Miele S., Dowding J., Liebermann E., Garry D., Rocha E.P.C, Bernheim A, Bikard D.
Cell Host and Microbes S1931-3128(22)00104-4 (2022)

Evolutionary and mechanistic diversity of Type I-F CRISPR-associated transposons
Klompe S, Jaber N, Bel L, Mohabir J, Bernheim A, Sternberg S.
Molecular Cell 82 (3), 616-628e5 (2022)

Before 2021 (start of the lab), relevant publications

Prokaryotic viperins produce diverse antiviral molecules
Bernheim A., Millman A., Ofir G., Meitav G., Abraham C., Shomar H., Rosenberg M., Tal N., Melamed S., Amitai G., Sorek R.
Nature, 589, 120-124 (2021)

Bacterial retrons function in anti- phage defense
Millman A*, Bernheim A*, Stokar-Avihail A.*, Fedorenko T., Voichek M., Leavitt A., Sorek R.
Cell, 183 (6), 1551-1561 (2020)

The bacterial pan-immune system: anti-phage defense as a community resource
Bernheim A, Sorek R
Nature Reviews Microbiology 18, 113–119 (2020)

Atypical organizations and epistatic interactions of CRISPRs and cas clusters in genomes and their mobile gemetic elements
Bernheim A, Bikard D, Touchon M, Rocha EPC:
Nucleic Acids Research 48 (2), 748-760 (2020)

A matter of background: DNA repair, pathways as a possible cause for the sparse distribution of CRISPR–Cas, systems in bacteria
Bernheim A, Bikard D, Touchon M, Rocha EPC
Philosophical Transactions of the Royal Society B 374 (1772), 2018008 (2019)

Inhibition of NHEJ repair by type II-A CRISPR-Cas systems
Bernheim A, Calvo-Villaman A, Basier C, Cui L, Rocha EPC, Touchon M, Bikard D,
Nature Communications 8 (1), 1-9 (2017)