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Adventitious Virus Detection in Cells by High-Throughput Sequencing of Newly Synthesized RNAs: Unambiguous Differentiation of Cell Infection from Carryover of Viral Nucleic Acids.

Cheval J, Muth E, Gonzalez G, Coulpier M, Beurdeley P, Cruveiller S, Eloit M.

mSphere. 2019 Jun 5;4(3). pii: e00298-19. doi: 10.1128/mSphere.00298-19.


The Arginine Deiminase Operon Is Responsible for a Fitness Trade-Off in Extended-Spectrum-β-Lactamase-Producing Strains of Escherichia coli.

Billard-Pomares T, Clermont O, Castellanos M, Magdoud F, Royer G, Condamine B, Fouteau S, Barbe V, Roche D, Cruveiller S, Médigue C, Pognard D, Glodt J, Dion S, Rigal O, Picard B, Denamur E, Branger C.

Antimicrob Agents Chemother. 2019 Jul 25;63(8). pii: e00635-19. doi: 10.1128/AAC.00635-19. Print 2019 Aug.


Complete Genome Sequence of Bradyrhizobium sp. Strain ORS3257, an Efficient Nitrogen-Fixing Bacterium Isolated from Cowpea in Senegal.

Le Quéré A, Gully D, Teulet A, Navarro E, Gargani D, Fardoux J, Cruveiller S, Neyra M, Giraud E, Krasova Wade T.

Microbiol Resour Announc. 2019 Jan 17;8(3). pii: e01449-18. doi: 10.1128/MRA.01449-18. eCollection 2019 Jan.


Author Correction: Parallels between experimental and natural evolution of legume symbionts.

Clerissi C, Touchon M, Capela D, Tang M, Cruveiller S, Genthon C, Lopez-Roques C, Parker MA, Moulin L, Masson-Boivin C, Rocha EPC.

Nat Commun. 2018 Nov 2;9(1):4641. doi: 10.1038/s41467-018-07205-x.


Extended-spectrum β-lactamase-encoding genes are spreading on a wide range of Escherichia coli plasmids existing prior to the use of third-generation cephalosporins.

Branger C, Ledda A, Billard-Pomares T, Doublet B, Fouteau S, Barbe V, Roche D, Cruveiller S, Médigue C, Castellanos M, Decré D, Drieux-Rouze L, Clermont O, Glodt J, Tenaillon O, Cloeckaert A, Arlet G, Denamur E.

Microb Genom. 2018 Sep;4(9). doi: 10.1099/mgen.0.000203. Epub 2018 Aug 6.


Genomic study of a novel magnetotactic Alphaproteobacteria uncovers the multiple ancestry of magnetotaxis.

Monteil CL, Perrière G, Menguy N, Ginet N, Alonso B, Waisbord N, Cruveiller S, Pignol D, Lefèvre CT.

Environ Microbiol. 2018 Dec;20(12):4415-4430. doi: 10.1111/1462-2920.14364. Epub 2018 Oct 16.


Transcriptome Profiles of Nod Factor-independent Symbiosis in the Tropical Legume Aeschynomene evenia.

Gully D, Czernic P, Cruveiller S, Mahé F, Longin C, Vallenet D, François P, Nidelet S, Rialle S, Giraud E, Arrighi JF, DasGupta M, Cartieaux F.

Sci Rep. 2018 Jul 19;8(1):10934. doi: 10.1038/s41598-018-29301-0.


Parallels between experimental and natural evolution of legume symbionts.

Clerissi C, Touchon M, Capela D, Tang M, Cruveiller S, Genthon C, Lopez-Roques C, Parker MA, Moulin L, Masson-Boivin C, Rocha EPC.

Nat Commun. 2018 Jun 11;9(1):2264. doi: 10.1038/s41467-018-04778-5. Erratum in: Nat Commun. 2018 Nov 2;9(1):4641.


Expansion of the SOS regulon of Vibrio cholerae through extensive transcriptome analysis and experimental validation.

Krin E, Pierlé SA, Sismeiro O, Jagla B, Dillies MA, Varet H, Irazoki O, Campoy S, Rouy Z, Cruveiller S, Médigue C, Coppée JY, Mazel D.

BMC Genomics. 2018 May 21;19(1):373. doi: 10.1186/s12864-018-4716-8.


The genomic and transcriptomic basis of the potential of Lactobacillus plantarum A6 to improve the nutritional quality of a cereal based fermented food.

Turpin W, Weiman M, Guyot JP, Lajus A, Cruveiller S, Humblot C.

Int J Food Microbiol. 2018 Feb 2;266:346-354. doi: 10.1016/j.ijfoodmicro.2017.10.011. Epub 2017 Oct 6.


MicroScope-an integrated resource for community expertise of gene functions and comparative analysis of microbial genomic and metabolic data.

Médigue C, Calteau A, Cruveiller S, Gachet M, Gautreau G, Josso A, Lajus A, Langlois J, Pereira H, Planel R, Roche D, Rollin J, Rouy Z, Vallenet D.

Brief Bioinform. 2019 Jul 19;20(4):1071-1084. doi: 10.1093/bib/bbx113.


DNA Adenine Methyltransferase (Dam) Overexpression Impairs Photorhabdus luminescens Motility and Virulence.

Payelleville A, Lanois A, Gislard M, Dubois E, Roche D, Cruveiller S, Givaudan A, Brillard J.

Front Microbiol. 2017 Sep 1;8:1671. doi: 10.3389/fmicb.2017.01671. eCollection 2017.


Genomic and Transcriptomic Analysis of Growth-Supporting Dehalogenation of Chlorinated Methanes in Methylobacterium.

Chaignaud P, Maucourt B, Weiman M, Alberti A, Kolb S, Cruveiller S, Vuilleumier S, Bringel F.

Front Microbiol. 2017 Sep 1;8:1600. doi: 10.3389/fmicb.2017.01600. eCollection 2017.


Strand-specific transcriptomes of Enterohemorrhagic Escherichia coli in response to interactions with ground beef microbiota: interactions between microorganisms in raw meat.

Galia W, Leriche F, Cruveiller S, Garnier C, Navratil V, Dubost A, Blanquet-Diot S, Thevenot-Sergentet D.

BMC Genomics. 2017 Aug 3;18(1):574. doi: 10.1186/s12864-017-3957-2.


Complete Genome Sequence of Bradyrhizobium sp. ORS285, a Photosynthetic Strain Able To Establish Nod Factor-Dependent or Nod Factor-Independent Symbiosis with Aeschynomene Legumes.

Gully D, Teulet A, Busset N, Nouwen N, Fardoux J, Rouy Z, Vallenet D, Cruveiller S, Giraud E.

Genome Announc. 2017 Jul 27;5(30). pii: e00421-17. doi: 10.1128/genomeA.00421-17.


Recruitment of a Lineage-Specific Virulence Regulatory Pathway Promotes Intracellular Infection by a Plant Pathogen Experimentally Evolved into a Legume Symbiont.

Capela D, Marchetti M, Clérissi C, Perrier A, Guetta D, Gris C, Valls M, Jauneau A, Cruveiller S, Rocha EPC, Masson-Boivin C.

Mol Biol Evol. 2017 Oct 1;34(10):2503-2521. doi: 10.1093/molbev/msx165.


Conservation and diversity of the IrrE/DdrO-controlled radiation response in radiation-resistant Deinococcus bacteria.

Blanchard L, Guérin P, Roche D, Cruveiller S, Pignol D, Vallenet D, Armengaud J, de Groot A.

Microbiologyopen. 2017 Aug;6(4). doi: 10.1002/mbo3.477. Epub 2017 Apr 11.


An antimicrobial peptide-resistant minor subpopulation of Photorhabdus luminescens is responsible for virulence.

Mouammine A, Pages S, Lanois A, Gaudriault S, Jubelin G, Bonabaud M, Cruveiller S, Dubois E, Roche D, Legrand L, Brillard J, Givaudan A.

Sci Rep. 2017 Mar 2;7:43670. doi: 10.1038/srep43670.


MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes.

Vallenet D, Calteau A, Cruveiller S, Gachet M, Lajus A, Josso A, Mercier J, Renaux A, Rollin J, Rouy Z, Roche D, Scarpelli C, Médigue C.

Nucleic Acids Res. 2017 Jan 4;45(D1):D517-D528. doi: 10.1093/nar/gkw1101. Epub 2016 Nov 29.


Experimental evolution of rhizobia may lead to either extra- or intracellular symbiotic adaptation depending on the selection regime.

Marchetti M, Clerissi C, Yousfi Y, Gris C, Bouchez O, Rocha E, Cruveiller S, Jauneau A, Capela D, Masson-Boivin C.

Mol Ecol. 2017 Apr;26(7):1818-1831. doi: 10.1111/mec.13895. Epub 2016 Nov 12.


Tempo and mode of genome evolution in a 50,000-generation experiment.

Tenaillon O, Barrick JE, Ribeck N, Deatherage DE, Blanchard JL, Dasgupta A, Wu GC, Wielgoss S, Cruveiller S, Médigue C, Schneider D, Lenski RE.

Nature. 2016 Aug 11;536(7615):165-70. Epub 2016 Aug 1.


Adhesion, Biofilm Formation, and Genomic Features of Campylobacter jejuni Bf, an Atypical Strain Able to Grow under Aerobic Conditions.

Bronnec V, Turoňová H, Bouju A, Cruveiller S, Rodrigues R, Demnerova K, Tresse O, Haddad N, Zagorec M.

Front Microbiol. 2016 Jun 30;7:1002. doi: 10.3389/fmicb.2016.01002. eCollection 2016.


Contrasting effects of historical contingency on phenotypic and genomic trajectories during a two-step evolution experiment with bacteria.

Plucain J, Suau A, Cruveiller S, Médigue C, Schneider D, Le Gac M.

BMC Evol Biol. 2016 Apr 23;16:86. doi: 10.1186/s12862-016-0662-8.


Draft Genome Sequence of Campylobacter jejuni Bf, an Atypical Strain Able To Grow under Aerobiosis.

Bronnec V, Haddad N, Cruveiller S, Hernould M, Tresse O, Zagorec M.

Genome Announc. 2016 Apr 7;4(2). pii: e00120-16. doi: 10.1128/genomeA.00120-16.


The revisited genome of Pseudomonas putida KT2440 enlightens its value as a robust metabolic chassis.

Belda E, van Heck RG, José Lopez-Sanchez M, Cruveiller S, Barbe V, Fraser C, Klenk HP, Petersen J, Morgat A, Nikel PI, Vallenet D, Rouy Z, Sekowska A, Martins Dos Santos VA, de Lorenzo V, Danchin A, Médigue C.

Environ Microbiol. 2016 Oct;18(10):3403-3424. doi: 10.1111/1462-2920.13230. Epub 2016 Apr 28.


In planta comparative transcriptomics of host-adapted strains of Ralstonia solanacearum.

Ailloud F, Lowe TM, Robène I, Cruveiller S, Allen C, Prior P.

PeerJ. 2016 Jan 5;4:e1549. doi: 10.7717/peerj.1549. eCollection 2016.


RNase J depletion leads to massive changes in mRNA abundance in Helicobacter pylori.

Redko Y, Galtier E, Arnion H, Darfeuille F, Sismeiro O, Coppée JY, Médigue C, Weiman M, Cruveiller S, De Reuse H.

RNA Biol. 2016;13(2):243-53. doi: 10.1080/15476286.2015.1132141.


Comparative genomics of 43 strains of Xanthomonas citri pv. citri reveals the evolutionary events giving rise to pathotypes with different host ranges.

Gordon JL, Lefeuvre P, Escalon A, Barbe V, Cruveiller S, Gagnevin L, Pruvost O.

BMC Genomics. 2015 Dec 23;16:1098. doi: 10.1186/s12864-015-2310-x.


Synonymous Genetic Variation in Natural Isolates of Escherichia coli Does Not Predict Where Synonymous Substitutions Occur in a Long-Term Experiment.

Maddamsetti R, Hatcher PJ, Cruveiller S, Médigue C, Barrick JE, Lenski RE.

Mol Biol Evol. 2015 Nov;32(11):2897-904. doi: 10.1093/molbev/msv161. Epub 2015 Jul 20.


Novel metabolic features in Acinetobacter baylyi ADP1 revealed by a multiomics approach.

Stuani L, Lechaplais C, Salminen AV, Ségurens B, Durot M, Castelli V, Pinet A, Labadie K, Cruveiller S, Weissenbach J, de Berardinis V, Salanoubat M, Perret A.

Metabolomics. 2014;10(6):1223-1238. doi: 10.1007/s11306-014-0662-x. Epub 2014 Apr 29.


The conserved nhaAR operon is drastically divergent between B2 and non-B2 Escherichia coli and is involved in extra-intestinal virulence.

Lescat M, Reibel F, Pintard C, Dion S, Glodt J, Gateau C, Launay A, Ledda A, Cruveiller S, Tourret J, Tenaillon O.

PLoS One. 2014 Sep 30;9(9):e108738. doi: 10.1371/journal.pone.0108738. eCollection 2014. Erratum in: PLoS One. 2015;10(3):e0118729. Cruvellier, Stephane [corrected to Cruveiller, Stephane].


Large chromosomal rearrangements during a long-term evolution experiment with Escherichia coli.

Raeside C, Gaffé J, Deatherage DE, Tenaillon O, Briska AM, Ptashkin RN, Cruveiller S, Médigue C, Lenski RE, Barrick JE, Schneider D.

MBio. 2014 Sep 9;5(5):e01377-14. doi: 10.1128/mBio.01377-14.


Transient hypermutagenesis accelerates the evolution of legume endosymbionts following horizontal gene transfer.

Remigi P, Capela D, Clerissi C, Tasse L, Torchet R, Bouchez O, Batut J, Cruveiller S, Rocha EP, Masson-Boivin C.

PLoS Biol. 2014 Sep 2;12(9):e1001942. doi: 10.1371/journal.pbio.1001942. eCollection 2014 Sep.


Characterization of a P1-like bacteriophage carrying an SHV-2 extended-spectrum β-lactamase from an Escherichia coli strain.

Billard-Pomares T, Fouteau S, Jacquet ME, Roche D, Barbe V, Castellanos M, Bouet JY, Cruveiller S, Médigue C, Blanco J, Clermont O, Denamur E, Branger C.

Antimicrob Agents Chemother. 2014 Nov;58(11):6550-7. doi: 10.1128/AAC.03183-14. Epub 2014 Aug 18.


RNA sequencing and proteogenomics reveal the importance of leaderless mRNAs in the radiation-tolerant bacterium Deinococcus deserti.

de Groot A, Roche D, Fernandez B, Ludanyi M, Cruveiller S, Pignol D, Vallenet D, Armengaud J, Blanchard L.

Genome Biol Evol. 2014 Apr;6(4):932-48. doi: 10.1093/gbe/evu069.


Evolutionary history and genetic parallelism affect correlated responses to evolution.

Le Gac M, Cooper TF, Cruveiller S, Médigue C, Schneider D.

Mol Ecol. 2013 Jun;22(12):3292-3303.


Epistasis and allele specificity in the emergence of a stable polymorphism in Escherichia coli.

Plucain J, Hindré T, Le Gac M, Tenaillon O, Cruveiller S, Médigue C, Leiby N, Harcombe WR, Marx CJ, Lenski RE, Schneider D.

Science. 2014 Mar 21;343(6177):1366-9. doi: 10.1126/science.1248688. Epub 2014 Mar 6.


Experimental evolution of nodule intracellular infection in legume symbionts.

Guan SH, Gris C, Cruveiller S, Pouzet C, Tasse L, Leru A, Maillard A, Médigue C, Batut J, Masson-Boivin C, Capela D.

ISME J. 2013 Jul;7(7):1367-77. doi: 10.1038/ismej.2013.24. Epub 2013 Feb 21.


Genomic analysis of smooth tubercle bacilli provides insights into ancestry and pathoadaptation of Mycobacterium tuberculosis.

Supply P, Marceau M, Mangenot S, Roche D, Rouanet C, Khanna V, Majlessi L, Criscuolo A, Tap J, Pawlik A, Fiette L, Orgeur M, Fabre M, Parmentier C, Frigui W, Simeone R, Boritsch EC, Debrie AS, Willery E, Walker D, Quail MA, Ma L, Bouchier C, Salvignol G, Sayes F, Cascioferro A, Seemann T, Barbe V, Locht C, Gutierrez MC, Leclerc C, Bentley SD, Stinear TP, Brisse S, Médigue C, Parkhill J, Cruveiller S, Brosch R.

Nat Genet. 2013 Feb;45(2):172-9. doi: 10.1038/ng.2517. Epub 2013 Jan 6.


Mutation rate dynamics in a bacterial population reflect tension between adaptation and genetic load.

Wielgoss S, Barrick JE, Tenaillon O, Wiser MJ, Dittmar WJ, Cruveiller S, Chane-Woon-Ming B, Médigue C, Lenski RE, Schneider D.

Proc Natl Acad Sci U S A. 2013 Jan 2;110(1):222-7. doi: 10.1073/pnas.1219574110. Epub 2012 Dec 17.


MicroScope--an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data.

Vallenet D, Belda E, Calteau A, Cruveiller S, Engelen S, Lajus A, Le Fèvre F, Longin C, Mornico D, Roche D, Rouy Z, Salvignol G, Scarpelli C, Thil Smith AA, Weiman M, Médigue C.

Nucleic Acids Res. 2013 Jan;41(Database issue):D636-47. doi: 10.1093/nar/gks1194. Epub 2012 Nov 27.


Genome sequence of the marine bacterium Marinobacter hydrocarbonoclasticus SP17, which forms biofilms on hydrophobic organic compounds.

Grimaud R, Ghiglione JF, Cagnon C, Lauga B, Vaysse PJ, Rodriguez-Blanco A, Mangenot S, Cruveiller S, Barbe V, Duran R, Wu LF, Talla E, Bonin P, Michotey V.

J Bacteriol. 2012 Jul;194(13):3539-40. doi: 10.1128/JB.00500-12.


Mutation Rate Inferred From Synonymous Substitutions in a Long-Term Evolution Experiment With Escherichia coli.

Wielgoss S, Barrick JE, Tenaillon O, Cruveiller S, Chane-Woon-Ming B, Médigue C, Lenski RE, Schneider D.

G3 (Bethesda). 2011 Aug 1;1(3):183-186.


The genome of the obligate endobacterium of an AM fungus reveals an interphylum network of nutritional interactions.

Ghignone S, Salvioli A, Anca I, Lumini E, Ortu G, Petiti L, Cruveiller S, Bianciotto V, Piffanelli P, Lanfranco L, Bonfante P.

ISME J. 2012 Jan;6(1):136-45. doi: 10.1038/ismej.2011.110. Epub 2011 Aug 25.


Chemical evolution of a bacterium's genome.

Marlière P, Patrouix J, Döring V, Herdewijn P, Tricot S, Cruveiller S, Bouzon M, Mutzel R.

Angew Chem Int Ed Engl. 2011 Jul 25;50(31):7109-14. doi: 10.1002/anie.201100535. Epub 2011 Jun 27. No abstract available.


Complete nucleotide sequence of plasmid pTN48, encoding the CTX-M-14 extended-spectrum β-lactamase from an Escherichia coli O102-ST405 strain.

Billard-Pomares T, Tenaillon O, Le Nagard H, Rouy Z, Cruveiller S, Médigue C, Arlet G, Denamur E, Branger C.

Antimicrob Agents Chemother. 2011 Mar;55(3):1270-3. doi: 10.1128/AAC.01108-10. Epub 2010 Dec 20.


Molecular and evolutionary bases of within-patient genotypic and phenotypic diversity in Escherichia coli extraintestinal infections.

Levert M, Zamfir O, Clermont O, Bouvet O, Lespinats S, Hipeaux MC, Branger C, Picard B, Saint-Ruf C, Norel F, Balliau T, Zivy M, Le Nagard H, Cruveiller S, Chane-Woon-Ming B, Nilsson S, Gudelj I, Phan K, Ferenci T, Tenaillon O, Denamur E.

PLoS Pathog. 2010 Sep 30;6(9):e1001125. doi: 10.1371/journal.ppat.1001125. Erratum in: PLoS Pathog. 2011 Jun;7(6). doi:10.1371/annotation/700dcb3b-3475-49a1-9064-d9d070cda7be. Cruvellier, Stéphane[corrected to Cruveiller, Stéphane].


Structure, function, and evolution of the Thiomonas spp. genome.

Arsène-Ploetze F, Koechler S, Marchal M, Coppée JY, Chandler M, Bonnefoy V, Brochier-Armanet C, Barakat M, Barbe V, Battaglia-Brunet F, Bruneel O, Bryan CG, Cleiss-Arnold J, Cruveiller S, Erhardt M, Heinrich-Salmeron A, Hommais F, Joulian C, Krin E, Lieutaud A, Lièvremont D, Michel C, Muller D, Ortet P, Proux C, Siguier P, Roche D, Rouy Z, Salvignol G, Slyemi D, Talla E, Weiss S, Weissenbach J, Médigue C, Bertin PN.

PLoS Genet. 2010 Feb 26;6(2):e1000859. doi: 10.1371/journal.pgen.1000859.


MicroScope: a platform for microbial genome annotation and comparative genomics.

Vallenet D, Engelen S, Mornico D, Cruveiller S, Fleury L, Lajus A, Rouy Z, Roche D, Salvignol G, Scarpelli C, Médigue C.

Database (Oxford). 2009;2009:bap021. Epub 2009 Nov 25.


Experimental evolution of a plant pathogen into a legume symbiont.

Marchetti M, Capela D, Glew M, Cruveiller S, Chane-Woon-Ming B, Gris C, Timmers T, Poinsot V, Gilbert LB, Heeb P, Médigue C, Batut J, Masson-Boivin C.

PLoS Biol. 2010 Jan 12;8(1):e1000280. doi: 10.1371/journal.pbio.1000280.

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