참고문헌 (66)

1. Alberdi, Antton, Aizpurua, Ostaizka, Bohmann, Kristine, Zepeda-Mendoza, Marie Lisandra, Gilbert, M. Thomas P.. Do Vertebrate Gut Metagenomes Confer Rapid Ecological Adaptation?. Trends in ecology & evolution, vol.31, no.9, 689-699.

   상세보기

2. Amato, Katherine R, Sanders, Jon G, Song, Se Jin, Nute, Michael, Metcalf, Jessica L, Thompson, Luke R, Morton, James T, Amir, Amnon, McKenzie, Valerie J, Humphrey, Gregory, Gogul, Grant, Gaffney, James, Baden, Andrea L, Britton, Gillian A O, Cuozzo, Frank P, Di Fiore, Anthony, Dominy, Nathaniel J, Goldberg, Tony L, Gomez, Andres, Kowalewski, Martin M, Lewis, Rebecca J, Link, Andres, Sauther, Michelle L, Tecot, Stacey, White, Bryan A, Nelson, Karen E, Stumpf, Rebecca M, Knight, Rob, Leigh, Steven R. Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes. The ISME journal : multidisciplinary journal of microbial ecology, vol.13, no.3, 576-587.

   상세보기

3. Amato, Katherine R., Leigh, Steven R., Kent, Angela, Mackie, Roderick I., Yeoman, Carl J., Stumpf, Rebecca M., Wilson, Brenda A., Nelson, Karen E., White, Bryan A., Garber, Paul A.. The Gut Microbiota Appears to Compensate for Seasonal Diet Variation in the Wild Black Howler Monkey (Alouatta pigra). Microbial ecology, vol.69, no.2, 434-443.

   상세보기

4. Bano, Nasreen, deRae Smith, Angelique, Bennett, William, Vasquez, Lydia, Hollibaugh, James T.. Dominance of Mycoplasma in the guts of the Long-Jawed Mudsucker, Gillichthys mirabilis, from five California salt marshes. Environmental microbiology, vol.9, no.10, 2636-2641.

   상세보기

5. Benhamed, S., Guardiola, F.A., Mars, M., Esteban, M.A.. Pathogen bacteria adhesion to skin mucus of fishes. Veterinary microbiology, vol.171, no.1, 1-12.

   상세보기

6. Benjamini, Yoav, Hochberg, Yosef. Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing. Journal of the Royal Statistical Society. Series B (Methodological), vol.57, no.1, 289-300.

   상세보기

7. Bolnick, Daniel I., Snowberg, Lisa K., Hirsch, Philipp E., Lauber, Christian L., Org, Elin, Parks, Brian, Lusis, Aldons J., Knight, Rob, Caporaso, J. Gregory, Svanbäck, Richard. Individual diet has sex-dependent effects on vertebrate gut microbiota. Nature communications, vol.5, 4500-.

   상세보기

8. Bolyen, Evan, Rideout, Jai Ram, Dillon, Matthew R., Bokulich, Nicholas A., Abnet, Christian C., Al-Ghalith, Gabriel A., Alexander, Harriet, Alm, Eric J., Arumugam, Manimozhiyan, Asnicar, Francesco, Bai, Yang, Bisanz, Jordan E., Bittinger, Kyle, Brejnrod, Asker, Brislawn, Colin J., Brown, C. Titus, Callahan, Benjamin J., Caraballo-Rodríguez, Andrés Mauricio, Chase, John, Cope, Emily K., Da Silva, Ricardo, Diener, Christian, Dorrestein, Pieter C., Douglas, Gavin M., Durall, Daniel M., Duvallet, Claire, Edwardson, Christian F., Ernst, Madeleine, Estaki, Mehrbod, Fouquier, Jennifer, Gauglitz, Julia M., Gibbons, Sean M., Gibson, Deanna L., Gonzalez, Antonio, Gorlick, Kestrel, Guo, Jiarong, Hillmann, Benjamin, Holmes, Susan, Holste, Hannes, Huttenhower, Curtis, Huttley, Gavin A., Janssen, Stefan, Jarmusch, Alan K., Jiang, Lingjing, Kaehler, Benjamin D., Kang, Kyo Bin, Keefe, Christopher R., Keim, Paul, Kelley, Scott T., Knights, . Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature biotechnology, vol.37, no.9, 1091-1091.

   상세보기

9. Bordenstein, Seth R., Theis, Kevin R.. Host Biology in Light of the Microbiome: Ten Principles of Holobionts and Hologenomes. PLoS biology, vol.13, no.8, e1002226-.

   상세보기

10. Boutin, Sébastien, Sauvage, Christopher, Bernatchez, Louis, Audet, Céline, Derome, Nicolas. Inter Individual Variations of the Fish Skin Microbiota: Host Genetics Basis of Mutualism?. PloS one, vol.9, no.7, e102649-.

    상세보기

11. BROOKS, B. W., MURRAY, R. G. E.. Nomenclature for "Micrococcus radiodurans" and Other Radiation-Resistant Cocci: Deinococcaceae fam. nov. and Deinococcus gen. nov., Including Five Species. International journal of systematic bacteriology, vol.31, no.3, 353-360.

    상세보기

12. Callahan, Benjamin J, McMurdie, Paul J, Rosen, Michael J, Han, Andrew W, Johnson, Amy Jo A, Holmes, Susan P. DADA2: High resolution sample inference from Illumina amplicon data. Nature methods, vol.13, no.7, 581-583.

    상세보기

13. Carrier, Tyler J., Reitzel, Adam M.. The Hologenome Across Environments and the Implications of a Host-Associated Microbial Repertoire. Frontiers in microbiology, vol.8, 802-.

    상세보기

14. Chiarello, Marlène, Auguet, Jean-Christophe, Bettarel, Yvan, Bouvier, Corinne, Claverie, Thomas, Graham, Nicholas A. J., Rieuvilleneuve, Fabien, Sucré, Elliot, Bouvier, Thierry, Villéger, Sébastien. Skin microbiome of coral reef fish is highly variable and driven by host phylogeny and diet. Microbiome, vol.6, no.1, 147-.

    상세보기

15. Le “barcoding alimentaire”: Développement d’un nouvel outil d’écologie moléculaire pour les milieux d’eau douce. Exemple au travers de l’étude de la zone hybride Durance entre les deux Chondrostomes français Corse E. 

16. Corse, Emmanuel, Pech, Nicolas, Sinama, Melthide, Costedoat, Caroline, Chappaz, Rémi, Gilles, André. When Anthropogenic River Disturbance Decreases Hybridisation between Non-Native and Endemic Cyprinids and Drives an Ecomorphological Displacement towards Juvenile State in Both Species. PloS one, vol.10, no.11, e0142592-.

    상세보기

17. Donaldson, Gregory P., Lee, S. Melanie, Mazmanian, Sarkis K.. Gut biogeography of the bacterial microbiota. Nature reviews. Microbiology, vol.14, no.1, 20-32.

    상세보기

18. Draghi II, Andrew, Popov, Vsevolod L., Kahl, Melissa M., Stanton, James B., Brown, Corrie C., Tsongalis, Gregory J., West, A. Brian, Frasca Jr., Salvatore. Characterization of “ Candidatus Piscichlamydia salmonis” (Order Chlamydiales ), a Chlamydia-Like Bacterium Associated With Epitheliocystis in Farmed Atlantic Salmon ( Salmo salar ). Journal of clinical microbiology, vol.42, no.11, 5286-5297.

    상세보기

19. Hydrobiologia Filipe A. F. 331 719 2013 Vulnerability of stream biota to climate change in Mediterranean climate regions: A synthesis of ecological responses and conservation challenges 

20. 10.1046/j.0962-1083.2001.01411.x 

    

21. Fuhrman, Jed A.. Microbial community structure and its functional implications. Nature, vol.459, no.7244, 193-199.

    상세보기

22. Galan, Maxime, Razzauti, Maria, Bard, Emilie, Bernard, Maria, Brouat, Carine, Charbonnel, Nathalie, Dehne-Garcia, Alexandre, Loiseau, Anne, Tatard, Caroline, Tamisier, Lucie, Vayssier-Taussat, Muriel, Vignes, Helene, Cosson, Jean-François. 16S rRNA Amplicon Sequencing for Epidemiological Surveys of Bacteria in Wildlife. mSystems, vol.1, no.4, e00032-16-.

    상세보기

23. Gould, Alison L., Zhang, Vivian, Lamberti, Lisa, Jones, Eric W., Obadia, Benjamin, Korasidis, Nikolaos, Gavryushkin, Alex, Carlson, Jean M., Beerenwinkel, Niko, Ludington, William B.. Microbiome interactions shape host fitness. Proceedings of the National Academy of Sciences of the United States of America, vol.115, no.51, E11951-E11960.

    상세보기

24. Guevara Soto, Maricruz, Vidondo, Beatriz, Vaughan, Lloyd, Seth-Smith, Helena M. B., Nufer, Lisbeth, Segner, Helmut, Rubin, Jean-Francois, Schmidt-Posthaus, Heike. The emergence of epitheliocystis in the upper Rhone region: evidence for Chlamydiae in wild and farmed salmonid populations. Archives of microbiology, vol.198, no.4, 315-324.

    상세보기

25. Guivier, Emmanuel, Gilles, André, Pech, Nicolas, Duflot, Nicolas, Tissot, Laurence, Chappaz, Rémi. Canals as ecological corridors and hybridization zones for two cyprinid species. Hydrobiologia, vol.830, no.1, 1-16.

    상세보기

26. Guivier, Emmanuel, Martin, Jean-François, Pech, Nicolas, Ungaro, Arnaud, Chappaz, Rémi, Gilles, André. Microbiota Diversity Within and Between the Tissues of Two Wild Interbreeding Species. Microbial ecology, vol.75, no.3, 799-810.

    상세보기

27. Hao, Yao Tong, Wu, Shan Gong, Jakovlić, Ivan, Zou, Hong, Li, Wen Xiang, Wang, Gui Tang. Impacts of diet on hindgut microbiota and short‐chain fatty acids in grass carp (Ctenopharyngodon idellus). Aquaculture research, vol.48, no.11, 5595-5605.

    상세보기

28. Hao, Yao Tong, Wu, Shan Gong, Xiong, Fan, Tran, Ngoc T., Jakovlić, Ivan, Zou, Hong, Li, Wen Xiang, Wang, Gui Tang. Succession and Fermentation Products of Grass Carp ( Ctenopharyngodon idellus ) Hindgut Microbiota in Response to an Extreme Dietary Shift. Frontiers in microbiology, vol.8, 1585-.

    상세보기

29. Holben, W.E., Williams, P., Saarinen, M., Särkilahti, L.K., Apajalahti, J.H.A.. Phylogenetic Analysis of Intestinal Microflora Indicates a Novel Mycoplasma Phylotype in Farmed and Wild Salmon. Microbial ecology, vol.44, no.2, 175-185.

    상세보기

30. The IUCN Red List of Threatened Species. Version 2018-1 IUCN 2018 

31. Kashinskaya, E.N., Simonov, E.P., Kabilov, M.R., Izvekova, G.I., Andree, K.B., Solovyev, M.M.. Diet and other environmental factors shape the bacterial communities of fish gut in an eutrophic lake. Journal of applied microbiology, vol.125, no.6, 1626-1641.

    상세보기

32. Kozich, James J., Westcott, Sarah L., Baxter, Nielson T., Highlander, Sarah K., Schloss, Patrick D.. Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform. Applied and environmental microbiology, vol.79, no.17, 5112-5120.

    상세보기

33. Langille, Morgan G. I., Zaneveld, Jesse, Caporaso, J. Gregory, McDonald, Daniel, Knights, Dan, Reyes, Joshua A., Clemente, Jose C., Burkepile, Deron E., Vega Thurber, Rebecca L., Knight, Rob, Beiko, Robert G., Huttenhower, Curtis. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nature biotechnology, vol.31, no.9, 814-821.

    상세보기

34. Li, Peng, Yin, Yu-Long, Li, Defa, Woo Kim, Sung, Wu, Guoyao. Amino acids and immune function. The British journal of nutrition, vol.98, no.2, 237-252.

    상세보기

35. Li, Xuemei, Yan, Qingyun, Ringø, Einar, Wu, Xingbing, He, Yongfeng, Yang, Deguo. The influence of weight and gender on intestinal bacterial community of wild largemouth bronze gudgeon ( Coreius guichenoti , 1874). BMC microbiology, vol.16, 191-.

    상세보기

36. Liu, Han, Guo, Xianwu, Gooneratne, Ravi, Lai, Ruifang, Zeng, Cong, Zhan, Fanbin, Wang, Weimin. The gut microbiome and degradation enzyme activity of wild freshwater fishes influenced by their trophic levels. Scientific reports, vol.6, 24340-.

    상세보기

37. Louca, Stilianos, Doebeli, Michael, Parfrey, Laura Wegener. Correcting for 16S rRNA gene copy numbers in microbiome surveys remains an unsolved problem. Microbiome, vol.6, no.1, 41-.

    상세보기

38. Lowrey, Liam, Woodhams, Douglas C., Tacchi, Luca, Salinas, Irene. Topographical Mapping of the Rainbow Trout (Oncorhynchus mykiss) Microbiome Reveals a Diverse Bacterial Community with Antifungal Properties in the Skin. Applied and environmental microbiology, vol.81, no.19, 6915-6925.

    상세보기

39. Lozupone, Catherine, Knight, Rob. UniFrac: a New Phylogenetic Method for Comparing Microbial Communities. Applied and environmental microbiology, vol.71, no.12, 8228-8235.

    상세보기

40. Mandal, Siddhartha, Van Treuren, Will, White, Richard A., Eggesbø, Merete, Knight, Rob, Peddada, Shyamal D.. Analysis of composition of microbiomes: a novel method for studying microbial composition. Microbial ecology in health and disease, vol.26, 10.3402/mehd.v26.27663-.

    상세보기

41. vegan: Community ecology package. R package version 2.4‐1 Oksanen J. 2016 

42. Paliy, O., Shankar, V.. Application of multivariate statistical techniques in microbial ecology. Molecular ecology, vol.25, no.5, 1032-1057.

    상세보기

43. Parks, Donovan H., Tyson, Gene W., Hugenholtz, Philip, Beiko, Robert G.. STAMP: statistical analysis of taxonomic and functional profiles. Bioinformatics, vol.30, no.21, 3123-3124.

    상세보기

44. Pratte, Zoe A., Besson, Marc, Hollman, Rebecca D., Stewart, Frank J.. The Gills of Reef Fish Support a Distinct Microbiome Influenced by Host-Specific Factors. Applied and environmental microbiology, vol.84, no.9, e00063-18-e00063-18.

    상세보기

45. Price, Morgan N., Dehal, Paramvir S., Arkin, Adam P.. FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments. PloS one, vol.5, no.3, e9490-.

    상세보기

46. Quast, Christian, Pruesse, Elmar, Yilmaz, Pelin, Gerken, Jan, Schweer, Timmy, Yarza, Pablo, Peplies, Jörg, Glöckner, Frank Oliver. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic acids research, vol.41, no.d1, D590-D596.

    상세보기

47. R: A language and environment for statistical computing R Core Team 2016 

48. Read, Daniel S, Gweon, Hyun S, Bowes, Michael J, Newbold, Lindsay K, Field, Dawn, Bailey, Mark J, Griffiths, Robert I. Catchment-scale biogeography of riverine bacterioplankton. The ISME journal : multidisciplinary journal of microbial ecology, vol.9, no.2, 516-526.

    상세보기

49. Salinas, Irene. The Mucosal Immune System of Teleost Fish. Biology, vol.4, no.3, 525-539.

    상세보기

50. Sellyei, Boglárka, Molnár, Kálmán, Székely, Csaba. Diverse Chlamydia-like agents associated with epitheliocystis infection in two cyprinid fish species, the common carp (Cyprinus carpio L.) and the gibel carp (Carassius auratus gibelio L.). Acta veterinaria Hungarica, vol.65, no.1, 29-40.

    상세보기

51. Sevellec, Maelle, Derome, Nicolas, Bernatchez, Louis. Holobionts and ecological speciation: the intestinal microbiota of lake whitefish species pairs. Microbiome, vol.6, no.1, 47-.

    상세보기

52. Šimková, Andrea, Civáňová, Kristína, Gettová, Lenka, Gilles, André. Genomic Porosity between Invasive Chondrostoma nasus and Endangered Endemic Parachondrostoma toxostoma (Cyprinidae): The Evolution of MHC IIB Genes. PloS one, vol.8, no.6, e65883-.

    상세보기

53. Simon, Jean-Christophe, Marchesi, Julian R., Mougel, Christophe, Selosse, Marc-André. Host-microbiota interactions: from holobiont theory to analysis. Microbiome, vol.7, no.1, 5-.

    상세보기

54. Sylvain, François-Étienne, Cheaib, Bachar, Llewellyn, Martin, Gabriel Correia, Tiago, Barros Fagundes, Daniel, Luis Val, Adalberto, Derome, Nicolas. pH drop impacts differentially skin and gut microbiota of the Amazonian fish tambaqui ( Colossoma macropomum ). Scientific reports, vol.6, 32032-.

    상세보기

55. Tarnecki, Andrea M., Brennan, Nathan P., Schloesser, Ryan W., Rhody, Nicole R.. Shifts in the Skin-Associated Microbiota of Hatchery-Reared Common Snook Centropomus undecimalis During Acclimation to the Wild. Microbial ecology, vol.77, no.3, 770-781.

    상세보기

56. Tremaroli, Valentina, B채ckhed, Fredrik. Functional interactions between the gut microbiota and host metabolism. Nature, vol.489, no.7415, 242-249.

    상세보기

57. Uren Webster, Tamsyn M., Consuegra, Sofia, Hitchings, Matthew, Garcia de Leaniz, Carlos. Interpopulation Variation in the Atlantic Salmon Microbiome Reflects Environmental and Genetic Diversity. Applied and environmental microbiology, vol.84, no.16, e00691-18-.

    상세보기

58. Ursell, L.K., Clemente, J.C., Rideout, J.R., Gevers, D., Caporaso, J.G., Knight, R.. The interpersonal and intrapersonal diversity of human-associated microbiota in key body sites. The Journal of allergy and clinical immunology : official organ of American Academy of Allergy, vol.129, no.5, 1204-1208.

    상세보기

59. V철r철smarty, C. J., McIntyre, P. B., Gessner, M. O., Dudgeon, D., Prusevich, A., Green, P., Glidden, S., Bunn, S. E., Sullivan, C. A., Liermann, C. Reidy, Davies, P. M.. Global threats to human water security and river biodiversity. Nature, vol.467, no.7315, 555-561.

    상세보기

60. Wang, An R., Ran, Chao, Ringø, Einar, Zhou, Zhi G.. Progress in fish gastrointestinal microbiota research. Reviews in aquaculture, vol.10, no.3, 626-640.

    상세보기

61. Wang, Qiong, Garrity, George M., Tiedje, James M., Cole, James R.. Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy. Applied and environmental microbiology, vol.73, no.16, 5261-5267.

    상세보기

62. Wang, An R., Ran, Chao, Ringø, Einar, Zhou, Zhi G.. Progress in fish gastrointestinal microbiota research. Reviews in aquaculture, vol.10, no.3, 626-640.

    상세보기

63. Weiss, Sophie, Xu, Zhenjiang Zech, Peddada, Shyamal, Amir, Amnon, Bittinger, Kyle, Gonzalez, Antonio, Lozupone, Catherine, Zaneveld, Jesse R., Vázquez-Baeza, Yoshiki, Birmingham, Amanda, Hyde, Embriette R., Knight, Rob. Normalization and microbial differential abundance strategies depend upon data characteristics. Microbiome, vol.5, no.1, 27-.

    상세보기

64. Bacteriology of humans: An ecological perspective Wilson M. 2008 

65. Xing, Mengxin, Hou, Zhanhui, Yuan, Jianbo, Liu, Yuan, Qu, Yanmei, Liu, Bin. Taxonomic and functional metagenomic profiling of gastrointestinal tract microbiome of the farmed adult turbot (Scophthalmus maximus). FEMS microbiology ecology, vol.86, no.3, 432-443.

    상세보기

66. Yan, Qingyun, Li, Jinjin, Yu, Yuhe, Wang, Jianjun, He, Zhili, Van Nostrand, Joy D., Kempher, Megan L., Wu, Liyou, Wang, Yaping, Liao, Lanjie, Li, Xinghao, Wu, Shu, Ni, Jiajia, Wang, Chun, Zhou, Jizhong. Environmental filtering decreases with fish development for the assembly of gut microbiota. Environmental microbiology, vol.18, no.12, 4739-4754.

    상세보기