Publications

Google scholar citations

69. Gadoin E., Durand L., Guillou A., Crochemore S.,Bouvier T., Roque E., Dagorn L, Auguet J-C., Adingra A., Desnues C., Bettarel Y. (2021) Does the composition of the gut bacteriome change during the growth of tuna? Microorganisms. 27;9(6):1157. doi: 10.3390/microorganisms9061157.

68. Nebbak A., Monteil-Bouchard S. Bérenger J-M., Almeras L., Parola P., Desnues C. (2021) Virome diversity among mosquito populations in a sub-urban region of Marseille, France, Viruses, Apr 27;13(5):768. doi: 10.3390/v13050768.

Press article (in French) : LM-BdR et Var-08_05_2021-20

67. Piazzola J., Bruch W., Desnues C., Parent P., Yohia C., Canepa E. (2021) Influence of meteorological conditions and aerosol properties on the COVID-19 contamination of the population in coastal andcontinental areas in France: study of offshore and onshore winds. Atmosphere 12(4), 523; https://doi.org/10.3390/atmos12040523

66. Danko D., Bezdan D., Afshinnekoo E., Ahsanuddin S., Bhattacharya C., Butler D.J., Chng K.R., Donnellan D., Hecht J., Jackson K., Kuchin K., Karasikov M., Lyons A., Mak L., Meleshko D., Mustafa H., Mutai B.,Neches R.Y., Ng A., Nikolayeva O., Nikolayeva T., Png E., Ryon K., Sanchez J.L., Shaaban H., Sierra M.A.,Thomas D., Young B., Abudayyeh O.O, Alicea J., Bhattacharyya M., Blekhman R., Castro-Nallar E., Cañas A.M., Chatziefthimiou A.D., Crawford R.W., De Filippis F., Deng Y., Desnues C. et al., (2021) Global Genetic Cartography of Urban Metagenomes and Anti-Microbial Resistance. Cell. May 22:S0092-8674(21)00585-7. doi: 10.1016/j.cell.2021.05.002. Online ahead of print.PMID: 34043940

Press release:
Le monde 
Courrier International
Huffington Post
The New York Times

65. Bordigoni A, Bouchard S, Desnues C. (2021) Isolation and Characterization of Gardnerella Phage vB_Gva_AB1, a Bacteriophage Infecting a Clinical Strain of Gardnerella vaginalisMicrobiol Resour Announc. 25;10(12):e00053-21. doi: 10.1128/MRA.00053-21. PMID: 33766896; PMCID: PMC7996455.

64. Afshinnekoo E, Bhattacharya C, Burguete-García A, Castro-Nallar E, Deng Y, Desnues C, Dias-Neto E, Elhaik E, Iraola G, Jang S, Łabaj PP, Mason CE, Nagarajan N, Poulsen M, Prithiviraj B, Siam R, Shi T, Suzuki H, Werner J, Zambrano MM, Bhattacharyya M; MetaSUB Consortium (2021) COVID-19 drug practices risk antimicrobial resistance evolution. Lancet Microbe. 2(4):e135-e136. doi: 10.1016/S2666-5247(21)00039-2. Epub 2021 Feb 24. PMID: 33655229; PMCID: PMC7906697.

63. Bordigoni A, Motte A, Tissot-Dupont H, Colson P, Desnues C. (2021) Development and validation of a multiplex qPCR assay for detection and relative quantification of HPV16 and HPV18 E6 and E7 oncogenes. Sci Rep. 17;11(1):4039. doi: 10.1038/s41598-021-83489-2. PMID: 33597592; PMCID: PMC7889863.

62. Dupont S, Lokmer A, Corre E, Auguet JC, Petton B, Toulza E, Montagnani C, Tanguy G, Pecqueur D, Salmeron C, Guillou L, Desnues C, La Scola B, Bou Khalil J, de Lorgeril J, Mitta G, Gueguen Y, Escoubas JM. (2021) Oyster hemolymph is a complex and dynamic ecosystem hosting bacteria, protists and viruses. Anim Microbiome. 28;2(1):12. doi: 10.1186/s42523-020-00032-w. PMID: 33499958; PMCID:
PMC7807429.

61. Bordigoni A, Lo CI, Yimagou EK, Diop K, Nicaise B, Raoult D, Desnues C, Fenollar F. (2020) Megasphaera vaginalis sp. nov. and Anaerococcus vaginimassiliensis sp. nov., new bacteria isolated from vagina of French woman with bacterial vaginosis. New Microbes New Infect. 3;37:100706. doi: 10.1016/j.nmni.2020.100706. PMID: 32774867; PMCID: PMC7404545.

60. A. Bordigoni A, Lo CI, Yimagou EK, Diop K, Nicaise B, Raoult D, Desnues C,
Fenollar F. (2020) Two new bacteria isolated from vagina of a patient with vaginosis: Atopobium massiliense sp. nov. and Butyricimonas vaginalis sp. nov. New Microbes New Infect. 38: 2052-2975. https://doi.org/10.1016/j.nmni.2020.100771.

59. Chng KR, Li C, Bertrand D, Ng AHQ, Kwah JS, Low HM, Tong C, Natrajan M, Zhang MH, Xu L, Ko KKK, Ho EXP, Av-Shalom TV, Teo JWP, Khor CC; MetaSUB Consortium, Chen SL, Mason CE, Ng OT, Marimuthu K, Ang B, Nagarajan N. (2020) Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment. Nat Med. 26(6):941-951. doi: 10.1038/s41591-020-0894-4. Epub 2020 Jun 8. PMID: 32514171; PMCID: PMC7303012.

58. Edwards R., Vega A., Norman H., Ohaeri M., Levi K., Dinsdale E., Cinek O., Aziz R., McNair K, Barr J., Bibby K., Brouns S.J., Cazares A., de Jonge P., Desnues C., et al., (2019) Global phylogeography and ancient evolution of the widespread human gut virus crAssphage, Nature Microbiol 8. doi: 10.1038/s41564-019-0494-6.56.

57. Rascovan N., Sjögren K.-G., Kristiansen K., Nielsen R., Willerslev E., Desnues C., Rasmussen S. (2019) Emergence and spread of basal lineages of Y. pestis during the Neolithic decline, Cell. DOI:https://doi.org/10.1016/j.cell.2018.11.005

56. Roux S., Adriaenssens E., Dutilh B., Koonin E., Kropinski A., Krupovic M., Kuhn J., Lavigne R., Rodney Brister J., Varsani A., Amid C., Aziz R., Bordenstein S., Bork P., Breitbart M, Cochrane G., Daly R., Desnues C.,Duhaime M., Emerson J., Enault F., Fuhrman J., HingampP., Hugenholtz P., Hurwitz B., Ivanova N., Labonté J., Lee K.-B., Malmstrom R., Martinez-Garcia M., Mizrachi I., Ogata H., Páez-Espino D., Petit M.-A., Putonti C., Rattei T., Reyes A., Rodriguez-Valera F., Rosario K., Schriml L., Schulz F., Steward G., Sullivan M., Sunagawa S., Suttle C., Temperton B., Tringe S., Vega Thurber R., Webster N., Whiteson K., Wilhelm S. Wommack E., Woyke T., Wrighton K., Yilmaz P., Yoshida T., Young M., Yutin N., Allen L., Kyrpides N., Eloe-Fadrosh E. (2018) Minimum Information about Uncultivated Virus Genomes (MIUViG): a community consensus on standards and best practices for describing genome sequences from uncultivated viruses. Nature Biotechnology37(1): 29-37.

55. Rolland C., Andreani J., Cherif Louazani A., Aherfi S., Francis R., Rodrigues R., Santos Silva L., Sahmi D., Mougari S., Chelka N., Bekliz M., Silva L., Assis F., Dornas F., Bou Khalil J., Pagnier I., Desnues C., Levasseur A., Colson P., Abrahão J., La Scola B. (2019) Discovery and further studies on giant viruses at IHU Mediterranee Infection that modified the perception of the virosphere, Viruses 30;11(4).

54. Million M., Gaudin M., Menelotte C., Chasson L., Zeitoun M., Prudent E., Edouard S., Amphoux B., Fallet M., Cadoret F., Meresse S., Paganini J., Lepidi H., Michelle C., Robert C., La Scola B., Naquet P., Gorvel J.-P., Desnues C., Raoult D. (2019) Metagenomic Analysis of Microdissected Valvular Tissue for Etiologic Diagnosis of Blood Culture Negative Endocarditis, Clinical and Infect. Dis. 2019 Jul 15. pii: ciz655. doi: 10.1093/cid/ciz655

53. Gaudin M., Desnues C. (2018) Hybrid capture-based next generation sequencing and its application to human infectious diseases, Front Microb (in press)

52. Jacquemot L., Bettarel Y., Monjol J., Corre E., Halary S., Desnues C., Bouvier T., Ferrier-Pagès C., Baudoux AC. (2018) Therapeutic potential of a new jumbo phage that infects the coral pathogen Vibrio coralliilyticus, Front Microb, doi.org/10.3389/fmicb.2018.02501

51. Duraisamy R., Akiana J., Davoust B., Mediannikov O., Michelle C., Robert C., Parra H.J., Raoult D., Biagini P., Desnues C. (2018) Detection of novel RNA viruses from free-living gorillas, Republic of the Congo: genetic diversity of picobirnaviruses. Virus Genes, 54(2):256-271. doi: 10.1007/s11262-018-1543-6.

50. Bettarel Y, Halary S, Auguet JC, Mai CT, Bui VN, Bouvier T, Got P, Bouvier C, Monteil S, Desnues C (2018) Corallivory and the microbial debacle in two branching scleratinians. ISME Journal doi:10.1038/s41396-017-0033-5

49. Rascovan N., Huynh H., Chouin G., Adekola K., Georges-Zimmermann P., Signoli M., Desfosses Y., Aboudharam G., Drancourt M. and Desnues C. (2016) Tracing back ancient oral microbiomes and oral pathogens using dental pulps from ancient teeth, NPJ Biofilms and Microbiomes. 2 (6) doi:10.1038/s41522-016-0008-8

48. Halary S, Duraisamy R, Fancello L, Monteil-Bouchard S, Jardot P, Biagini P, Gouriet F, Raoult D, Desnues C. (2016) Novel Single-Stranded DNA Circular Viruses in Pericardial Fluid of Patient with Recurrent Pericarditis. Emerg Infect Dis. 22(10):1839-41. doi: 10.3201/eid2210.160052.

47. Rascovan N, Drancourt M, Desnues C. (2016) Ancient Yersinia pestis genomes for tracing the origins and spreading of plague past epidemics. Med Sci. 32(8-9):681-683. doi: 10.1051/medsci/20163208007.

46. Rascovan N, Duraisamy R, Desnues C. (2016) Metagenomics and the Human Virome in Asymptomatic Individuals. Annu Rev Microbiol. 70:125-141. doi: 10.1146/annurev-micro-102215-095431.

45. The MetaSUB International Consortium (2016) The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report. Microbiome. 2016;4:24.

44. Rascovan N, Telke A, Raoult D, Rolain JM, Desnues C. (2016) Exploring divergent antibiotic resistance genes in ancient metagenomes and discovery of a novel beta-lactamase family. Environ Microbiol Rep. 70:125-141. doi:10.1111/1758-2229.12453.

43. Temmam S. and Desnues C. (2016) Zoonotic viruses and emergence: how to monitor for surveillance ? Virologie. 20(4):231-244. doi:10.1684/vir.2016.0660

42. Temmam S., Khalil J.B., La Scola B., and Desnues C. (2016) A new asfarvirus infecting amoebae found in arthropods and their associated mammals. Virologie. 20(4):245-247. doi:10.1684/vir.2016.0661

41. Temmam S., Monteil-Bouchard S., Robert C., Baudoin J.P., Sambou M., Aubadie-Ladrix M., Labas N., Raoult D., Mediannikov O., and Desnues C. (2016) Characterization of Viral Communities of Biting Midges and Identification of Novel Thogotovirus Species and Rhabdovirus Genus. Viruses. 8(3):77

40. Rascovan N., Monteil-Bouchard S., Grob J.J., Gaudy C., Penicaud M., Raoult D. and Desnues C. (2016) Human polyomavirus-6 infecting lymph nodes of a patient with an angiolymphoid hyperplasia with eosinophilia or Kimura disease. Clin Infec Dis. 62(11):1419−21. doi:10.1093/cid/ciw135. 

39. Temmam S., Davoust B., Chaber A.L., Lignereux Y., Michelle C., Monteil-Bouchard S., Raoult D. and Desnues C. (2016) Screening for viral pathogens in African simian bushmeat seized at a French airport. Transb Emerging Dis. doi:10.1111/tbed.12481 

38. Temmam S., Monteil-Bouchard S., Sambou M., Aubadie-Ladrix M., Azza S., Decloquement P., Bou Y., Baudoin J.P., Jardot P., Robert C., La Scola B., Mediannikov O., Raoult D., and Desnues C. (2016) Faustovirus-like asfarvirus in hematophagous biting midges and their vertebrate hosts. Frontiers in Microb. 6:1406. doi:10.3389/fmicb.2015.01406.

37. Halary S., Temmam S. and Desnues C. (2016) Viral metagenomics: are we missing the giants? Current Op Microb. 31:34-43 doi: 10.1016/j.mib.2016.01.005

36. Temmam S., Monteil-Bouchard S., Robert C., Pascalis H., Michelle C., Jardot P., Charrel R., Raoult D., and Desnues C. (2015) Host-associated metagenomics: a guide to generate infectious RNA viromes. PLoS One 10(10): e0139810. doi:10.1371/journal.pone.0139810

35. Phan T.G., Desnues C., Switzer W.M., Djoko C.F., Schneider B.S., Deng X., Delwart E. (2015) Absence of giant blood Marseille-like virus DNA detection by polymerase chain reaction in plasma from healthy US blood donors and serum from multiply transfused patients from Cameroon Transfusion 55(6):1256-1262

34. Desnues C, and Raoult D. (2014) Reply to Sauvage et al. J Infect Dis. 210(12):2018-2019

33. Temmam S., Davoust B., Berenger J.M., Raoult D., and Desnues C. (2014) Viral metagenomics on animals as a tool for the detection of zoonoses prior to human infection? Int J Mol Sci. 10;15(6):10377-97.

32. Nguyen K.H., Bouvier T., Bouvier C., Doan N.H., Nguyen N.L., Rochelle-Newall E., Baudoux A.C., Desnues C., Reynaud S., Ferrier-Pages C., and Bettarel Y., (2014) High abundance of viruses in the mucus layer of scleratinian corals, Environmental Microbiology reports  6(6): 675-682 

31. Fancello L., Monteil S., Popgeorgiev N., Rivet R., Gouriet F., Fournier PE., Raoult D., and Desnues C. (2014) Viral communities associated with human pericardial fluids in idiopathic pericarditis, PLoS One, 1:9(4):e93367 

30. Appelt S., Fancello L., Le Bailly M., Raoult D., Drancourt M., Desnues C. (2014) Viruses in a 14th century coprolite, Applied and Environmental Microbiology, Feb 7. 

29. Hassani I., Robert C., Michelle C., Raoult D., Hocine H., and Desnues C. (2013) Non-contiguous finished genome sequence and description of Halopiger goleamassiliensis sp. nov., SIGS. 9(3):956-9. doi: 10.4056/sigs.4618288

28. Popgeorgiev N., Michel G., Lepidi H., Raoult D., and Desnues C. (2013) Marseillevirus adenitis in an 11-month-old child, Journal of Clinical Microbiology. 51(12):4102-5 

27. Popgeorgiev N., Colson P., Thuret I., Chiaroni J., Gallian P., Raoult D., and Desnues C. (2013) Marseillevirus prevalence in multitransfused patients suggest blood transmission, Journal of Clinical Virology. 58(4):722-5. 

26. Popgeorgiev N., Temmam S., Raoult D., and Desnues C. (2013) Describing the silent human virome with an emphasis on giant viruses, Intervirology. 56(6):395-412. 

25. Hassani I., Robert C., Michelle C., Raoult D., Hocine H., and Desnues C. (2013) Non-contiguous finished genome sequence and description of Halopiger djelfamassiliensis sp. nov., SIGS. 9(1):160-74 

24. Gaia M., Colson P., Desnues C., and La Scola B. (2013) The virophage concept, eLS, John Wiley & Sons, Inc., DOI: 10.1002/9780470015902.a0024410

23. Colson P., Fancello L., Gimenez G., Armougom F., Desnues C., Fournous G., Yoosuf N., Million M., La Scola B., and Raoult D. (2013) Evidence of the megavirome in humans, Journal of Clinical Virology 57(3):191-200

22. Popgeorgiev N., Boyer M., Fancello L., Monteil S., Robert C., Rivet R., Nappez C., Azza S., Chiaroni J., Raoult D., and Desnues C. (2013) Marseillevirus-like virus recovered from blood donated by asymptomatic humans, Journal of Infectious Diseases. 208(7):1042-50 

21. Fancello L., Trape S., Robert C., Boyer M., Popgeorgiev N., Raoult D., and Desnues C. (2013) Viruses in the desert: a metagenomic survey of viral communities in four perennial ponds of the Mauritanian Sahara, ISME Journal 7: 359-369.

20. Desnues C.*, La Scola B.*, Yutin N., Fournous G., Robert C., Azza S, Jardot P., Monteil S., Campocasso A., Koonin E., and Raoult D. (2012) Provirophages and transpovirons as the unique mobilome of giant viruses Proc Natl Acad Sci U S A.  109(44):18078-83. *contributed equally

19. Fancello L., Raoult D., and Desnues C. (2012) Computational tools for viral metagenomics and their application in clinical research, Virology. 20;434(2):162-74.

18. Parola P., Renvoisé A., Botelho-Nevers E., Lascola B., Desnues C., and Raoult D. (2012) Acanthamoeba polyphaga mimivirus Virophage Seroconversion in Travelers Returning from Laos, Emerg. Infect. Dis. 18(9):1500-2

17. Desnues C. and Raoult D. (2012) Virophages question the existence of satellites, Nature Rev. Microbiol. 10: 234

16. Desnues C., Boyer M., and Raoult D. (2012) Sputnik, a virophage infecting the viral domain of life, Advances in Virus Research. 83:63-89.

15. Fancello L., Desnues C., Raoult D., and Rolain J.M. (2011) Bacteriophages and diffusion of genes encoding antimicrobial resistance in cystic fibrosis sputum microbiota. J Antimicrob. Chemother. 66(11):2448-54.

14. Rolain J.M., Fancello L., Desnues C., and Raoult D. (2011) Bacteriophages as vehicles of the resistome in cystic fibrosis. J Antimicrob. Chemother. 66(11):2444-7

13. Boyer M., Azza S., Barrassi L., Klose T., Campocasso A., Pagnier I., Fournous G., Borg A., Robert C., Zhang X., Desnues C., Henrissat B., Rossmann M.G., La Scola B., and Raoult D. (2011) Mimivirus shows dramatic genome reduction after intraamoebal culture. Proc Natl Acad Sci U S A. 108(25):10296-301.

12. Desnues C. and Raoult D. (2010) Inside the lifestyle of the virophage, Intervirology. 53:304-309

11. Colson P., Richet H., Desnues C., Balique F., Moal V., Grob J.J., Berbis P., Lecoq H., Harlé J.R., Berland Y., Raoult D. (2010) Pepper mild mottle virus, a plant virus associated with specific immune responses, Fever, abdominal pains, and pruritus in humans. PLoS One. Apr 6;5(4):e10041.

10. Rodriguez-Brito B, Li L., Wegley L., Furlan M., Angly F., Breitbart M., Buchanan J., Desnues C., Dinsdale E., Edwards R., Felts B., Willner D., Haynes M., Liu H., Lipson D., Mahaffy J., Martin-Cuadrado A., Mira A., Nulton J., Pašic L., Rayhawk S., Rodriguez-Mueller J., Rodriguez-Valera F., Salamon P., Srinagesh S., Thingstad, T. F., Tran T., Thurber R. V., Willner D., Youle M. and Rohwer F. (2010) Viral and microbial community dynamics in four aquatic environments. ISME journal. 4(6):739-51

9. Angly F. E., Willner D.,  Prieto-Davó A., Edwards R. A., Schmieder R., Vega Thurber  R., Antonopoulos D. A., Barott K., Cottrell M. T., Desnues C., Dinsdale E. A., Furlan M., Haynes M., Henn M. R., Hu Y., Kirchman D. L., McDole T., McPherson J. D., Meyer F., Miller R. M., Mundt E., Naviaux R. K., Rodriguez-Mueller B., Stevens R., Wegley L., Zhang L., Zhu B., and Rohwer F. (2009) The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes. PLOS Computational Biology, 5 (12):e1000593.

8. Thurber R. V., Willner-Hall D., Rodriguez-Mueller B., Desnues C., Edwards R. A., Angly F., Dinsdale E., Kelly L., and Rohwer F. (2009) Metagenomic analysis of stressed coral holobionts. Environ Microbiol., 11 (8): 2148-2163.

7. Thurber R. V., Barott K., Willner D., Liu H., Rodriguez-Mueller B., Desnues C., Edwards R., Haynes M., Angly F., Kelly L., and Rohwer F. (2008) Metagenomic Analysis Indicates that Stressors Induce Production of Herpes-like Viruses in the Coral Porites Compressa PNAS, 105 (48): 18413-18418

6. LaScola B.*, Desnues C.*, Pagnier I., Robert C., Barrassi L., Fournous G., Merchat M., Suzan-Monti M., Forterre P., Koonin E., and Raoult D. (2008) The virophage as a unique parasite of the giant Mimivirus. Nature, 455: 100-104.* contributed equally

5. Dinsdale E., Edwards R., Hall D., Angly F., Breitbart M, Brulc J., Furlan M., Desnues C., Haynes M., Li L., McDaniel L., Moran M., Nelson K., Nilsson C., Olson R., Paul J., Rodriguez Brito B., Ruan Y., Swan B., Stevens R., Valentine D., Vega Thurber R., Wegley L., White B., and Rohwer F. (2008) Functional Metagenomic Profiling of Nine Biomes. Nature, 452: 629-632.

4. Desnues C., Rodriguez-Brito B., Rayhawk S., Kelley S., Tuong T., Haynes M., Liu H., Furlan M., Wegley L., Chau B., Ruan Y., Hall D., Angly F., Edwards RA., Vega Thurber R., R. Reid P., Siefert J., Souza V., Valentine DL., Swan BK, Breitbart M., and Rohwer F. (2008) Biodiversity and biogeography of phages in modern stromatolites and thrombolites. Nature, 452: 340-343.

3. Desnues C., Michotey V., and Bonin P. (2007) Seasonal and diurnal distributions of denitrifying and bacterial communities in a hypersaline microbial mat (Camargue, France). Water Research, 41(15): 3407-3419.

2. Goréguès C., Michotey V., and Bonin P. (2005) Molecular, biochemical and physiological approaches for understanding the ecology of denitrification. Microbial Ecology, 49(2): 198-208.

1. Goréguès C., Michotey V., and Bonin P. (2004) Isolation of hydrocarbonoclastic denitrifying bacteria from Berre microbial mats. Ophélia (Current Marine Biology Research), 58 (3): 263-270.