Publications

2020-present

72. Gauthier J, Marquis H, Paquet VE, Charette SJ, Levesque RC and Derome N (2021) Genomic Perspectives on Aeromonas salmonicida subsp. salmonicida Strain 890054 as a Model System for Pathogenicity Studies and Mitigation of Fish Infections. Front. Mar. Sci. 8:744052. doi: 10.3389/fmars.2021.744052

71. El Khoury, S.; Gauthier, J.; Bouslama, S.; Cheaib, B.; Giovenazzo, P.; Derome, N. Dietary Contamination with a Neonicotinoid (Clothianidin) Gradient Triggers Specific Dysbiosis Signatures of Microbiota Activity along the Honeybee (Apis mellifera) Digestive Tract. Microorganisms 2021, 9, 2283. https://doi.org/10.3390/microorganisms9112283

70. Lavoie C, Wellband K, Perreault A, Bernatchez L, Derome N. Artificial Rearing of Atlantic Salmon Juveniles for Supportive Breeding Programs Induces Long-Term Effects on Gut Microbiota after Stocking. Microorganisms. 2021 Sep 11;9(9):1932.

69. Émie, AG., François-Étienne, S., Sidki, B. et al. Microbiomes of clownfish and their symbiotic host anemone converge before their first physical contact. Microbiome 9, 109 (2021). https://doi.org/10.1186/s40168-021-01058-1

68. Gauthier J, Derome N. Evenness-Richness Scatter Plots: a Visual and Insightful Representation of Shannon Entropy Measurements for Ecological Community Analysis. mSphere. 2021 Apr 7;6(2):e01019-20.

67. Cheaib B, Seghouani H, Llewellyn MS, Vandal-Lenghan K , Mercier PL,Derome N. 2020. The yellow perch (Perca flavescens) microbiome revealed resistance to colonisation mostly associated with neutralism driven by rare taxa under cadmium disturbance. In press in Animal Microbiome.

66. Boilard A, Dubé CE, Gruet C, Mercière A,Hernandez-Agreda A  and Derome N. 2020. Defining Coral Bleaching as a Microbial Dysbiosis within the Coral Holobiont. Microorganisms 8, 1682.

65. Derome, N., & Filteau, M. (2020). A continuously changing selective context on microbial communities associated with fish, from egg to fork. Evolutionary applications, 13(6), 1298–1319. https://doi.org/10.1111/eva.13027

64. Bleau, N., Bouslama, S., Giovenazzo, P., & Derome, N. (2020). Dynamics of the Honeybee (Apis mellifera) Gut Microbiota Throughout the Overwintering Period in Canada. Microorganisms, 8(8), 1146. https://doi.org/10.3390/microorganisms8081146

63. Cheaib, B., Seghouani, H., Ijaz, U. Z., & Derome, N. (2020). Community recovery dynamics in yellow perch microbiome after gradual and constant metallic perturbations. Microbiome, 8(1), 14. https://doi.org/10.1186/s40168-020-0789-0

62. Sylvain, F. É., Holland, A., Bouslama, S., Audet-Gilbert, É., Lavoie, C., Val, A. L., & Derome, N. (2020). Fish Skin and Gut Microbiomes Show Contrasting Signatures of Host Species and Habitat. Applied and environmental microbiology, 86(16), e00789-20. https://doi.org/10.1128/AEM.00789-20

2010-2019

61. Sylvain FÉ, Holland A, Audet-Gilbert É, Luis Val A, Derome N. (2019) Amazon fish bacterial communities show structural convergence along widespread hydrochemical gradients. Mol Ecol. 2019 Jul 20. doi: 10.1111/mec.15184. [Epub ahead of print]

60. Gauthier J, Rouleau-Breton S, Charette SJ, Derome N. (2019) Stimulated Growth and Innate Immunity in Brook Charr (Salvelinus fontinalis) Treated with a General Probiotic (Bactocell®) and Two Endogenous Probiotics That Inhibit Aeromonas salmonicida In Vitro. Microorganisms. Jul 6;7(7). pii: E193.

59. Gauthier J, Lavoie C, Charette SJ, Derome N (2019). Chapter 2: Host-microbiota interactions and their importance in promoting growth and disease resistance in farmed salmonids. In: Microbial Communities in Aquaculture Ecosystems. Springer Verlag, ISBN 3030161897.

58. Vincent AT, Gauthier J, Charette SJ, Derome N (2019). Chapter 1: The rise and fall of antibiotics in aquaculture. In: Microbial Communities in Aquaculture Ecosystems. Springer Verlag, ISBN 3030161897.

57. Gauthier J, Vincent AT, Charette SJ, Derome N. (2018) A brief history of bioinformatics. Briefings in Bioinformatics, bby063. https://doi.org/10.1093/bib/bby063

​56. Lavoie C, Courcelle M, Redivo B, Derome N. (2018) Structural and compositional mismatch between captive and wild Atlantic salmon (Salmo salar) parrs’ gut microbiota highlights the relevance of integrating molecular ecology for management and conservation methods. Evol Appl.;00:1–15. https://doi.org/10.1111/eva.12658

55. El Khoury S, Rousseau A, Lecoeur A, Cheaib B, Bouslama S, Mercier P-L, Demey V, Castex M, Giovenazzo P and Derome N (2018) Deleterious Interaction Between Honeybees (Apis mellifera) and its Microsporidian Intracellular Parasite Nosema ceranae Was Mitigated by Administrating Either Endogenous or Allochthonous Gut Microbiota Strains. Front. Ecol. Evol. 6:58. https://doi.org/10.3389/fevo.2018.00058

54. Cheaib B., LeBoulch M., Mercier P.-L. and Derome N (2018).  Taxon-Function Decoupling as an Adaptive Signature of Lake Microbial Metacommunities Under a Chronic Polymetallic Pollution Gradient.  Frontiers in Microbiology 9:869. https://doi.org/10.3389/fmicb.2018.00869

53. Sylvain FE, Derome N. Vertically and horizontally transmitted microbial symbionts shape the gut microbiota ontogenesis of a skin-mucus feeding discus fish progeny. Sci Rep. 2017 Jul 12;7(1):5263. doi: 10.1038/s41598-017-05662-w.

52. Gauthier J., Vincent A.T., Charette S.J., and Derome N (2017). Strong Genomic and Phenotypic Heterogeneity in the Aeromonas Sobria Species Complex. Frontiers in Microbiology 8. https://doi.org/10.3389/fmicb.2017.02434.

51. Seghouani H., Garcia-Rangel C.E., Füller J., Gauthier J. and Derome N. (2017) Walleye Autochthonous Bacteria as Promising Probiotic Candidates against Flavobacterium columnare. Frontiers in Microbiology 18;8:1349.

50. Gauthier J, Charette SJ, Derome N.  2017.  Draft Genome Sequence of Pseudomonas fluorescens ML11A, an Endogenous Strain from Brook Charr with Antagonistic Properties Against Aeromonas salmonicida subsp. salmonicida.  Genome Announcements e01716-16.

49. Llewellyn MS, Leadbeater S, Garcia C, Sylvain FE, Custodio M, Ang KP, Powell F, Carvalho GR, Creer S, Elliot J, Derome, N. 2017. Parasitism perturbs the mucosal microbiome of Atlantic Salmon. Sci Rep Mar 7;7:43465. doi: 10.1038/srep43465.

48. Trudel MV, Vincent AT, Attéré SA, Labbé M, Derome N, Culley AI, Charrette S. 2016. Diversity of antibiotic-resistance genes in Canadian isolates of Aeromonas salmonicida subsp. salmonicida: dominance of pSN254b and discovery of pAsa8. Sci Rep. 6:35617.

47.  Sylvain, FE, Cheaib B, Llewellyn M, Correia T, Val AL, Derome N. pH drop impacts differentially skin and gut microbiota of the Amazonian fish tambaqui (Colossoma macropomum. Nat. Sci. Rep. 18;6:32032.

46. Alburaki M, Cheaib B, Quesnel L, Mercier PL, Chagnon M, Derome N. 2016. Performance of honeybee colonies located in neonicotinoid-treated and untreated cornfields in Quebec. J. App. Ent. doi: 10.1111/jen.12336.

45.    Vincent AT, Derome N, Boyle B, Culley A, Charette, SJ. 2016. Next-generation sequencing (NGS) in the microbiological world: how to make the most of your money. J. Microbiol. Meth. in press.

44.    Llewellyn MS, McGinnity P, Dionne M, Letourneau J, Thonier F, Carvalho GR, Creer S, Derome N. 2015. The biogeography of the atlantic salmon (Salmo salar) gut microbiome. ISME J. PMID: 26517698

43.    Samson-Robert O, Labrie G, Mercier PL, Chagnon M, Derome N, Fournier V. 2015. Increased Acetylcholinesterase Expression in Bumble Bees During Neonicotinoid-Coated Corn Sowing. Sci Rep. 5:12636

42.    Boutin S, Alburaki M, Mercier PL, Giovenazzo P, Derome, N. 2015. Differential gene expression between hygienic and non-hygienic honeybee (Apis mellifera L.) hives. in press at BMC Genomics.

41.     Alburaki M, Mercier PL, Boutin S, Loublier Y, Chagnon M, Derome N. 2015. Neonicotinoid-coated Zea mays seeds indirectly affect honeybee performance and pathogen susceptibility in field trials. PLoS One, 10(5):e0125790.

40.   Vincent AT, Tanaka K, Trudel M, Frenette M, Derome N, Charette S. 2015. Draft Genome Sequences of Two Aeromonas salmonicida subsp. salmonicida Isolates Harboring Plasmids Conferring Antibiotic Resistance. Accepted at FEMS Microbiology Letters.

39.   Emond-Rheault JG, Vincent AT, Trudel MV, Brochu F, Boyle B, Tanaka KH, Attéré SA, Jubinville É, Loch TP, Winters AD, Faisal M, Frenette M, Derome N, Charrette SJ. 2014. Variants of a genomic island in Aeromonas salmonicida subsp. salmonicida link isolates with their geographical origins. Vet. Microb. PMID: 25480167.

38.   Vincent AT, Boyle B, Derome N, Charette SJ. 2014. Improvement in the DNA sequencing of genomes bearing long repeated elements. J Microbiol Methods. 107:186-188.

37.   Llewellyn MS, Messenger LA, Luquetti AO, Garcia AL, Torrico F, Tavares SBN, Cheaib B, Derome N et al. 2015. Deep sequencing of the Trypanosoma cruzi GP63 surface proteases reveals diversity and diversifying selection among chronic and congenital Chagas disease patients. In press at PLoS NTD. 

36.   Vincent AT, Trudel MV, Paquet VE, Boyle B, Tanaka KH, Dallaire-Dufresne S, Daher RK, Frenette M, Derome N, Charette SJ. 2014. Detection of variants of the pRAS3, pAB5S9, and pSN254 plasmids in Aeromonas salmonicida subsp. salmonicida: multidrug-resistance, interspecies exchanges, and plasmid reshaping. Antimicrob Agents Chemother. 03730-14. 

35.   Sevellec M, Pavey SA, Boutin S, Filteau M, Derome N, and L Bernatchez. 2014. Microbiome investigation in the ecological speciation context of lake Whitefish (Coregonus clupeaformis) using next generation sequencing. J. Evol. Biol. 27:1029-46. 

34.   Llewellyn, M, Boutin, S, Hoseinifar, SH, and N Derome. 2014. Teleost microbiomes: progress towards their characterisation, manipulation and applications in aquaculture and fisheries. Frontiers in Microbiology 5:207.

33.    Boutin, S, Sauvage, C, Bernatchez, L, Audet, C and N Derome. 2014. Inter individual variations of the fish skin microbiota: host genetics basis of mutualism? PLoS One, 9:e102649. 

32.    Boutin, S, Audet, C and N Derome. 2013. Probiotic treatment by indigenous bacteria decreased mortality rate without disturbing the natural microbiota of Salvelinus fontinalis.” Can. J. Microbiol. 59:662-70.

31.    Boutin, S, Bernatchez, L, Audet, C and N Derome. 2013. Network analysis highlights complex interaction between pathogen, host and commensal microbiota. PLoS One 8:e84772.

30.    Laplante, K, Boutin, S and N Derome. 2013. Parallel changes of taxonomic interaction networks in lacustrine bacterial communities induced by a polymetallic perturbation. Ev. App. 6:643-59.

29.    Boutin S, Sevellec M, Pavey SA, Bernatchez, L and N Derome. A fast highly sensitive double-nested PCR-based method to screen fish immunobiomes. Mol. Ecol. Res. 12:1027-39.

28.    Sauvage C, Vagner M, Derome N, Audet C and L Bernatchez. 2012. Coding gene SNP mapping reveals QTL linked to growth and stress response in brook charr (Salvelinus fontinalis). G3 2: 707-720.

27.    Sauvage C, Vagner M, Derome N, Audet C and L Bernatchez. 2012. Coding gene SNP mapping and QTL detection for physiological reproductive traits in brook charr, Salvelinus fontinalis. G3 2: 379-392.

26.    Charette, SJ, Brochu F, Boyle, B, Filion, G, Tanaka, KH and N Derome. 2011. Draft Genome Sequence of the virulent strain 01-B526 of the fish pathogen Aeromonas salmonicida. J. Bact. 194: 722-723.

25.    Boutin S, Bernatchez L, Audet C and N Derome. 2012. Antagonistic effect of indigenous skin bacteria of brook charr (Salvelinus fontinalis) against Flavobacterium columnare and F. Psychrophilum. Vet. Biol. 155: 355-361.

24.      Laplante K and N Derome. 2011. Convergent changes in the taxonomical structure of microbial communities exposed to a similar environmental disturbance. Ecol. & Evol.1:489-501. 

23.      Renaut S, Maillet N Normandeau E, Sauvage C, Derome N, Rogers SM and L Bernatchez. 2011. The genetic basis of species boundaries: the lake whitefish case study. Philos Trans R Soc Lond B Biol Sci 367: 354-63.

22.      Sauvage C, Renaut S, Normandeau E, Derome N and L Bernatchez 2011. Investigating the role of natural selection on coding sequence evolution in salmonids through NGS data mining. Mol. Biol. Evol. 28: 2721.

21.      Bastide E, Cazemajor M, Ogereau D, Derome N, Hospital F and C Montchamp-Moreau. 2011. Fast rise and fall of selfish sex-ratio X chromosomes in Drosophila simulans: Spatio-temporal analysis of phenotypic and molecular data. Mol. Biol. Evol. 28: 2461-2470.

20.      Renaut S, Nolte AW, Rogers SM, Derome N and L Bernatchez. 2010. Gradients of ecological speciation, SNP signature of selection on standing genetic variation, and association with adaptive phenotypes in lake whitefish species pairs (Coregonus spp.). Mol. Ecol. 20:545-549. [CRSNG-LB].

19        Sauvage C, Derome N, Normandeau E, St-Cyr J, Audet C and L Bernatchez. 2010. Fast Transcriptional Responses to Domestication in the Brook Charr Salvelinus fontinalis. Genetics 185: 105-112..

18.      Bernatchez L, Renaut S, Whiteley AR, Campbell D, Derome N, Jeukens J, Landry L, Lu G, Nolte AW, Østbye K , Rogers SM, St-Cyr J. 2010. On the origin of species: Insights from the ecological genomics of whitefish. Philos Trans R Soc Lond B Biol Sci. 365: 1783-800..

2000-2009

17.      Whiteley, AR, Persaud, KN, Derome, N, Montgomerie, R, and L Bernatchez. 2009. Reduced sperm performance provides evidence for genomic incompatibilities between whitefish species pairs  (Coregonus sp.). J. Can. J. Zool. 87: 566-572.

16.      Whiteley AR, Derome N, Rogers SM, St-Cyr J, Laroche J, Labbe A, Nolte A, Renaut S, Jeukens J, Bernatchez L. The phenomics and expression quantitative trait locus mapping of brain transcriptomes regulating adaptive divergence in lake whitefish species pairs (Coregonus sp.). 2008, Genetics 180: 147-164.

15.      Derome, N. Bougas, B., Rogers S., Whiteley A. Labbe, A. Laroche, J. & L. Bernatchez. 2008. Pervasive sex-linked effects on transcription regulation as revealed by eQTLmapping in lake whitefish species pairs (Coregonussp, Salmonidae). Genetics. 179: 1903-1917.

14.      Derome, N., Baudry, E. Ogereau, D. Veuille, M. and C. Montchamp-Moreau. 2008. Large-scale non-adaptive selective sweep caused by synergy between two linked segregation distorter in Drosophila simulans. Mol Biol Evol. 25: 409-41613.      Derome, N., Baudry, E. Ogereau, D. Veuille, M. and C. Montchamp-Moreau. Large-scale non-adaptive selective sweep caused by synergy between two linked segregation distorter in Drosophila simulans. Mol Biol Evol, accepté 04/09/2007.

12.      Derome, N. and L. Bernatchez. The transcriptomics of ecological convergence between two limnetic coregonine fishes (Salmonidae). 2006. Mol Biol Evol, 23: 1-9.

11.       Baudry*, E., Derome*, N., Huet, M. and M. Veuille. Worldwide variation patterns in Drosophila simulans show unexpected differences between African populations. 2006. Genetics, 173: 759-67. *: co-premiers auteurs.

10.      Derome, N., Duchesne, P. and L. Bernatchez. Parallelism in gene transcription among sympatric lake whitefish (Coregonus clupeaformis Mitchill) ecotypes. 2006 Mol Ecol, 15: 1239-49.

9.        Derome, N., Metayer, K., Montchamp-Moreau, C. and M. Veuille. Signature of selective sweep associated with the evolution of sex-ratio drive in Drosophila simulans. 2004 Genetics, 166: 1357-66.

8.        Derome, N., Chen, W.J., Dettai, A., Bonillo, C., and G. Lecointre. Phylogeny of antarctic dragon fishes (Bathydraconidae, Notothenioidei,Teleostei) and related families based on their anatomy and two mitochondrial genes. 2002. Mol Phyl Evol, 24: 139-52.

7.        Mousset, S., Derome, N. and M. Veuille. A test of neutrality and constant population size based on the mismatch distribution. 2004. Mol Biol Evol, 21: 724-731. 6.

6.        Mousset, S. and N. Derome. Molecular polymorphism in Drosophila melanogaster and Drosophila. simulans: What did we learn from recent studies ? 2004. Genetica, 120: 79-86.

5.        Jutier, D., Derome, N. and C. Montchamp-Moreau. Sex-ratio drive in Drosophila simulans. 2004. Genetica, 120: 87-99.

4.        Atlan, A., Capillon, C., Derome N. Couvet D. and C. Montchamp-Moreau. The evolution of autosomal suppressors of sex-ratio drive in Drosophila simulans. 2003. Genetica, 117: 47-58.

3,        Veuille M., Baudry E., Cobb M., Derome N. and E. Gravot. Historicity and the population genetics of Drosophila melanogaster and D. simulans. 2004. Genetica, 120: 61-70.

2.      Pisano, E., Mazzei, F. Derome, N., Ozouf-Costaz, C., Hureau, J. C. and G. Di Prisco. Cytogenetics of the bathydraconid fish Gymnodraco acuticeps (Perciformes, Notothenioidei) from Terra Nova Bay, Ross Sea. 2001. Polar Biol, 24: 846-852.