Anderson MJ (2001) A new method for non‐parametric multivariate analysis of variance. Austral Ecol 26(1):32–46
Anderson MJ (2004) PERMDISP: a FORTRAN computer program for permutational analysis of multivariate dispersions (for any two-factor ANOVA design) using permutation tests. Department of Statistics, University of Auckland, New Zealand, 24.
Aykanat T, Heath JW, Dixon B, Heath DD (2012a) Additive, non-additive and maternal effects of cytokine transcription in response to immunostimulation with Vibrio vaccine in Chinook salmon (Oncorhynchus tshawytscha). Immunogenetics 64(9):691–703
Google Scholar
Aykanat T, Bryden CA, Heath DD (2012b) Sex‐biased genetic component distribution among populations: additive genetic and maternal contributions to phenotypic differences among populations of Chinook salmon. J Evolut Biol 25(4):682–690
Google Scholar
Bates JM, Mittge E, Kuhlman J, Baden KN, Cheesman SE, Guillemin K (2006) Distinct signals from the microbiota promote different aspects of zebrafish gut differentiation. Developmental Biol 297(2):374–386
Google Scholar
Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc: Ser B (Methodol) 57(1):289–300
Berg G, Rybakova D, Fischer D, Cernava T, Vergès MCC, Charles T et al. (2020) Microbiome definition re-visited: old concepts and new challenges. Microbiome 8(1):1–22
Bernatchez L, Dodson JJ (1987) Relationship between bioenergetics and behavior in anadromous fish migrations. Can J Fish Aquat Sci 44(2):399–407
Google Scholar
Blackwell CN, Picard CR, Foy M (1999) Smolt productivity of off-channel habitat in the Chilliwack River watershed. Watershed Restoration Program.
Bokulich NA, Robeson M, Dillon MR (2020) bokulich-lab/RESCRIPt. Zenodo. https://doi.org/10.5281/zenodo.3891931
Bolnick DI, Snowberg LK, Hirsch PE, Lauber CL, Knight R, Caporaso JG et al. (2014a) Individuals’ diet diversity influences gut microbial diversity in two freshwater fish (threespine stickleback and Eurasian perch). Ecol Lett 17(8):979–987
Google Scholar
Bolnick DI, Snowberg LK, Hirsch PE, Lauber CL, Org E, Parks B et al. (2014b) Individual diet has sex-dependent effects on vertebrate gut microbiota. Nat Commun 5:4500
Google Scholar
Bolnick DI, Snowberg LK, Caporaso JG, Lauber C, Knight R, Stutz WE (2014c) Major H istocompatibility C omplex class II b polymorphism influences gut microbiota composition and diversity. Mol Ecol 23(19):4831–45. Oct
Google Scholar
Booman M, Forster I, Vederas JC, Groman DB, Jones SR (2018) Soybean meal-induced enteritis in Atlantic salmon (Salmo salar) and Chinook salmon (Oncorhynchus tshawytscha) but not in pink salmon (O. gorbuscha). Aquaculture 483:238–243
Google Scholar
Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA et al. (2019) Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nat Biotechnol 37(8):852–857
Google Scholar
Boyle CA, Lavkulich L, Schreier H, Kiss E (1997) Changes in land cover and subsequent effects on Lower Fraser Basin ecosystems from 1827 to 1990. Environ Manag 21(2):185–196
Google Scholar
Bradford MJ (1995) Comparative review of Pacific salmon survival rates. Can J Fish Aquat Sci 52(6):1327–1338
Google Scholar
Brüssow H (2020) The relationship between the host genome, microbiome, and host phenotype. Environ Microbiol 22(4):1170–1173
Google Scholar
Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP (2016) DADA2: high-resolution sample inference from Illumina amplicon data. Nat methods 13(7):581–583
Google Scholar
Carlson SM, Seamons TR (2008) A review of quantitative genetic components of fitness in salmonids: implications for adaptation to future change. Evolut Appl 1(2):222–238
Google Scholar
Cederholm CJ, Kunze MD, Murota T, Sibatani A (1999) Pacific salmon carcasses: essential contributions of nutrients and energy for aquatic and terrestrial ecosystems. Fisheries 24(10):6–15
Google Scholar
Ciric M, Waite D, Draper J, Jones JB (2019) Characterization of mid-intestinal microbiota of farmed Chinook salmon using 16S rRNA gene metabarcoding. Arch Biol Sci 71(4):577–587
Google Scholar
Chen C, Huang X, Fang S, Yang H, He M, Zhao Y et al. (2018) Contribution of host genetics to the variation of microbial composition of cecum lumen and feces in pigs. Front Microbiol 9:2626
Google Scholar
Davis NM, Proctor DM, Holmes SP, Relman DA, Callahan BJ (2018) Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data. Microbiome 6(1):226
Google Scholar
De Goffau MC, Lager S, Salter SJ, Wagner J, Kronbichler A, Charnock-Jones DS et al. (2018) Recognizing the reagent microbiome. Nat Microbiol 3(8):851–853
Google Scholar
Dhariwal A, Chong J, Habib S, King IL, Agellon LB, Xia J (2017) Microbiome Analyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data. Nucleic acids Res 45(W1):W180–W188
Google Scholar
Difford GF, Plichta DR, Løvendahl P, Lassen J, Noel SJ, Højberg O et al. (2018) Host genetics and the rumen microbiome jointly associate with methane emissions in dairy cows. PloS Genet 14(10):e1007580
Google Scholar
Dvergedal H, Sandve SR, Angell IL, Klemetsdal G, Rudi K (2020) Association of gut microbiota with metabolism in juvenile Atlantic salmon. Microbiome 8(1):1–8. Dec
Google Scholar
Dwidar M, Monnappa AK, Mitchell RJ (2012) The dual probiotic and antibiotic nature of Bdellovibrio bacteriovorus. BMB Rep. 45(2):71–78
Google Scholar
Eschmeyer WN, Fong JD (2015) Species by family/subfamily in the Catalog of Fishes. California Academy of Sciences, San Francisco, CA
Evenden AJ, Grayson TH, Gilpin ML, Munn CB (1993) Renibacterium salmoninarum and bacterial kidney disease—the unfinished jigsaw. Annu Rev Fish Dis 3:87–104
Google Scholar
Falconer DS, Mackay TFC (1996) Addison-Wesley Longman Limited; Essex, UK: 1996. Introduction to quantitative genetics.
FAO – Global Capture Production 1950-2017. Fisheries and Aquaculture Information and Statistics Branch – accessed on 21/01/2020
Fogarty C, Burgess CM, Cotter PD, Cabrera‐Rubio R, Whyte P, Smyth C et al. (2019) Diversity and composition of the gut microbiota of Atlantic salmon (Salmo salar) farmed in Irish waters. J Appl Microbiol 127(3):648–657
Google Scholar
Galindo-Villegas J, García-Moreno D, de Oliveira S, Meseguer J, Mulero V (2012) Regulation of immunity and disease resistance by commensal microbes and chromatin modifications during zebrafish development. Proc Natl Acad Sci 109(39):E2605–E2614
Google Scholar
Garcia de Leaniz C, Fleming IA, Einum S, Verspoor E, Jordan WC, Consuegra S et al. (2007) A critical review of adaptive genetic variation in Atlantic salmon: implications for conservation. Biol Rev 82(2):173–211
Google Scholar
Ghanbari M, Kneifel W, Domig KJ (2015) A new view of the fish gut microbiome: advances from next-generation sequencing. Aquaculture 448:464–475
Google Scholar
Gilmour KM, DiBattista JD, Thomas JB (2005) Physiological causes and consequences of social status in salmonid fish. Integr Comp Biol 45(2):263–273
Google Scholar
Gjedrem T (1983) Genetic variation in quantitative traits and selective breeding in fish and shellfish. Aquaculture 33(1-4):51–72
Google Scholar
Glover KA, Solberg MF, McGinnity P, Hindar K, Verspoor E, Coulson MW et al. (2017) Half a century of genetic interaction between farmed and wild Atlantic salmon: Status of knowledge and unanswered questions. Fish Fish 18(5):890–927
Google Scholar
Gomez-Uchida D, Seeb JE, Habicht C, Seeb LW (2012) Allele frequency stability in large, wild exploited populations over multiple generations: insights from Alaska sockeye salmon (Oncorhynchus nerka). Can J Fish Aquat Sci 69(5):916–929
Google Scholar
Gordon A, Hannon G (2017) Fastx-toolkit. FASTQ/A short-reads pre-processing tools. 2010. Unpublished available online at: http://hannonlab.cshl.edu/fastx_toolkit.
Goodrich JK, Di Rienzi SC, Poole AC, Koren O, Walters WA, Caporaso JG et al. (2014a) Conducting a microbiome study. Cell 158(2):250–262
Google Scholar
Goodrich JK, Waters JL, Poole AC, Sutter JL, Koren O, Blekhman R et al. (2014b) Human genetics shape the gut microbiome. Cell 159(4):789–799
Google Scholar
Goodrich JK, Davenport ER, Beaumont M, Jackson MA, Knight R, Ober C (2016) Genetic determinants of the gut microbiome in UK twins. Cell host microbe 19(5):731–743
Google Scholar
Gould AL, Zhang V, Lamberti L, Jones EW, Obadia B, Korasidis N et al. (2018) Microbiome interactions shape host fitness. Proc Natl Acad Sci 115(51):E11951–E11960
Google Scholar
Ham DG (1996) Patterns of channel change on Chilliwack River, British Columbia (Doctoral dissertation, University of British Columbia).
Hammer Ø, Harper DA, Ryan PD (2001) PAST: Paleontological statistics software package for education and data analysis. Palaeontologia Electron 4(1):9
Hansen TF (2006) The evolution of genetic architecture. Annu Rev Ecol Evol Syst 37:123–157
Google Scholar
He X, Chaganti SR, Heath DD (2018) Population-specific responses to interspecific competition in the gut microbiota of two Atlantic Salmon (Salmo salar) populations. Microb Ecol 75(1):140–151
Google Scholar
Heath DD, Shrimpton JM, Hepburn RI, Jamieson SK, Brode SK, Docker MF (2006) Population structure and divergence using microsatellite and gene locus markers in Chinook salmon (Oncorhynchus tshawytscha) populations. Can J Fish Aquat Sci 63(6):1370–1383
Google Scholar
Ingerslev HC, Strube ML, von Gersdorff Jørgensen L, Dalsgaard I, Boye M, Madsen L (2014) Diet type dictates the gut microbiota and the immune response against Yersinia ruckeri in rainbow trout (Oncorhynchus mykiss). Fish shellfish Immunol 40(2):624–633
Google Scholar
Janowitz‐Koch I, Rabe C, Kinzer R, Nelson D, Hess MA, Narum SR (2018) Long‐term evaluation of fitness and demographic effects of a Chinook Salmon supplementation program. Evolut Appl 12(3):456–469
Google Scholar
Kaltz O, Shykoff JA (1998) Local adaptation in host–parasite systems. Heredity 81(4):361–370
Google Scholar
Kawecki TJ, Ebert D (2004) Conceptual issues in local adaptation. Ecol Lett 7(12):1225–1241
Google Scholar
Kim BR, Shin J, Guevarra R, Lee JH, Kim DW, Seol KH et al. (2017) Deciphering diversity indices for a better understanding of microbial communities. J Microbiol Biotechnol 27(12):2089–2093
Google Scholar
Koehler ME, Fresh KL, Beauchamp DA, Cordell JR, Simenstad CA, Seiler DE (2006) Diet and bioenergetics of lake-rearing juvenile Chinook salmon in Lake Washington. Trans Am Fish Soc 135(6):1580–1591
Google Scholar
Kurilshikov A, Wijmenga C, Fu J, Zhernakova A (2017) Host genetics and gut microbiome: challenges and perspectives. Trends Immunol 38(9):633–647
Google Scholar
Larsen AM, Mohammed HH, Arias CR (2014) Characterization of the gut microbiota of three commercially valuable warmwater fish species. J Appl Microbiol 116(6):1396–1404
Google Scholar
Leamy LJ, Kelly SA, Nietfeldt J, Legge RM, Ma F, Hua K et al. (2014) Host genetics and diet, but not immunoglobulin A expression, converge to shape compositional features of the gut microbiome in an advanced intercross population of mice. Genome Biol 15(12):552
Google Scholar
Lenth R, Singmann H, Love J, Buerkner P, Herve P (2018) Emmeans: Estimated marginal means, aka least-squares means R package version 1.1
Lex A, Gehlenborg N, Strobelt H, Vuillemot R, Pfister H (2014) UpSet: visualization of intersecting sets. IEEE Trans Vis computer Graph 20(12):1983–1992
Google Scholar
Li T, Long M, Gatesoupe FJ, Zhang Q, Li A, Gong X (2015) Comparative analysis of the intestinal bacterial communities in different species of carp by pyrosequencing. Microb Ecol 69(1):25–36
Google Scholar
Li W, Liu J, Tan H, Yang C, Ren L, Liu Q et al. (2018) Genetic Effects on the Gut Microbiota Assemblages of Hybrid Fish From Parents With Different Feeding Habits. Front Microbiol 9:2972. 4
Google Scholar
Llewellyn MS, Boutin S, Hoseinifar SH, Derome N (2014) Teleost microbiomes: the state of the art in their characterization, manipulation and importance in aquaculture and fisheries. Front Microbiol 5:207
Google Scholar
Llewellyn MS, McGinnity P, Dionne M, Letourneau J, Thonier F, Carvalho GR et al. (2016) The biogeography of the Atlantic salmon (Salmo salar) gut microbiome. ISME J 10(5):1280–1284
Google Scholar
Lynch M, Walsh B (1998) Genetics and analysis of quantitative traits. Sunderland, MA: Sinauer; Jan.
Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J 17(1):10–12
Google Scholar
Metcalfe NB, Valdimarsson SK, Morgan IJ (2003) The relative roles of domestication, rearing environment, prior residence and body size in deciding territorial contests between hatchery and wild juvenile salmon. J Appl Ecol 40(3):535–544
Google Scholar
Milligan-Myhre K, Small CM, Mittge EK, Agarwal M, Currey M, Cresko WA et al. (2016) Innate immune responses to gut microbiota differ between oceanic and freshwater threespine stickleback populations. Dis Models Mechanisms 9(2):187–198
Google Scholar
Minich JJ, Poore GD, Jantawongsri K, Johnston C, Bowie K, Bowman J et al. (2020) Microbial ecology of Atlantic salmon (Salmo salar) hatcheries: impacts of the built environment on fish mucosal microbiota. Appl Environ Microbiol 86(12):e00411–e00420
Google Scholar
Narum SR, Schultz TL, Van Doornik DM, Teel D (2008) Localized genetic structure persists in wild populations of Chinook salmon in the John Day River despite gene flow from outside sources. Trans Am Fish Soc 137(6):1650–1656
Google Scholar
Navarrete P, Magne F, Araneda C, Fuentes P, Barros L, Opazo R et al. (2012) PCR-TTGE analysis of 16S rRNA from rainbow trout (Oncorhynchus mykiss) gut microbiota reveals host-specific communities of active bacteria. PloS one 7(2):e31335
Google Scholar
Nayak SK (2010) Role of gastrointestinal microbiota in fish. Aquac Res 41(11):1553–1573
Google Scholar
Nelson JS, Grande TC, Wilson MV (2016) Fishes of the World. John Wiley and Sons.
Nikouli E, Meziti A, Antonopoulou E, Mente E, Kormas KA (2018) Gut bacterial communities in geographically distant populations of farmed sea bream (Sparus aurata) and sea bass (Dicentrarchus labrax). Microorganisms 6(3):92
Google Scholar
Nikouli E, Meziti A, Antonopoulou E, Mente E, Kormas KA (2019) Host-Associated Bacterial Succession during the Early Embryonic Stages and First Feeding in Farmed Gilthead Sea Bream (Sparus aurata). Genes 10(7):483
Google Scholar
Nikouli E, Meziti A, Smeti E, Antonopoulou E, Mente E, Kormas KA (2020) Gut Microbiota of Five Sympatrically Farmed Marine Fish Species in the Aegean Sea. Microbial Ecology 1-11.
Oh S, Choi D, Cha CJ (2019) Ecological processes underpinning microbial community structure during exposure to subinhibitory level of triclosan. Sci Rep. 9(1):1–12
Ohlberger J, Ward EJ, Schindler DE, Lewis B (2018) Demographic changes in Chinook salmon across the Northeast Pacific Ocean. Fish Fish 19(3):533–546
Google Scholar
Palstra FP, Ruzzante DE (2010) A temporal perspective on population structure and gene flow in Atlantic salmon (Salmo salar) in Newfoundland, Canada. Can J Fish Aquat Sci 67(2):225–242
Google Scholar
Panteli N, Mastoraki M, Nikouli E, Lazarina M, Antonopoulou E, Kormas KA (2020) Imprinting statistically sound conclusions for gut microbiota in comparative animal studies: A case study with diet and teleost fishes. Comp Biochem Physiol Part D: Genomics Proteom 36:100738
Google Scholar
Parshukov AN, Kashinskaya EN, Simonov EP, Hlunov OV, Izvekova GI, Andree KB et al. (2019) Variations of the intestinal gut microbiota of farmed rainbow trout, Oncorhynchus mykiss (Walbaum), depending on the infection status of the fish. J Appl Microbiol 127(2):379–395
Google Scholar
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P et al. (2012) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic acids Res 41(D1):D590–D596
Google Scholar
Quinn TP (2018) The behavior and ecology of Pacific salmon and trout. University of Washington press.
Quinn TP, Unwin MJ, Kinnison MT (2000) Evolution of temporal isolation in the wild: genetic divergence in timing of migration and breeding by introduced chinook salmon populations. Evolution 54(4):1372–1385
Google Scholar
R Core Team (2016) R development core team. RA Lang. Environ Stat Comput 55(265), 275–286
Ren T, Boutin S, Humphries MM, Dantzer B, Gorrell JC, Coltman DW et al. (2017) Seasonal, spatial, and maternal effects on gut microbiome in wild red squirrels. Microbiome 5(1):163
Google Scholar
Riiser ES, Haverkamp TH, Varadharajan S, Borgan Ø, Jakobsen KS, Jentoft S et al. (2020) Metagenomic shotgun analyses reveal complex patterns of intra-and interspecific variation in the intestinal microbiomes of codfishes. Appl Environ Microbiol 86(6):e02788–19. Mar 2
Google Scholar
Roeselers G, Mittge EK, Stephens WZ, Parichy DM, Cavanaugh CM, Guillemin K et al. (2011) Evidence for a core gut microbiota in the zebrafish. ISME J 5(10):1595–1608. https://doi.org/10.1038/ismej.2011.38
Google Scholar
Romero J, Ringø E, Merrifield DL (2014) The gut microbiota of fish. Aquaculture nutrition: Gut health, probiotics and prebiotics 75-100.
Rosshart SP, Vassallo BG, Angeletti D, Hutchinson DS, Morgan AP, Takeda K et al. (2017) Wild mouse gut microbiota promotes host fitness and improves disease resistance. Cell 171(5):1015–1028
Google Scholar
Rothschild D, Weissbrod O, Barkan E, Kurilshikov A, Korem T, Zeevi D et al. (2018) Environment dominates over host genetics in shaping human gut microbiota. Nature 555(7695):210–215
Google Scholar
Rounsefell GA (1958) Anadromy in North American Salmonidae. US Government Printing Office.
Savolainen O, Lascoux M, Merilä J (2013) Ecological genomics of local adaptation. Nat Rev Genet 14(11):807–820
Google Scholar
Schmidt V, Amaral-Zettler L, Davidson J, Summerfelt S, Good C (2016) Influence of fishmeal-free diets on microbial communities in Atlantic salmon (Salmo salar) recirculation aquaculture systems. Appl Environ Microbiol 82(15):4470–4481
Google Scholar
Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS et al. (2011) Metagenomic biomarker discovery and explanation. Genome Biol 12(6):1–18
Google Scholar
Semova I, Carten JD, Stombaugh J, Mackey LC, Knight R, Farber SA et al. (2012) Microbiota regulate intestinal absorption and metabolism of fatty acids in the zebrafish. Cell host microbe 12(3):277–288
Google Scholar
Semeniuk CA, Capelle PM, Dender MG, Devlin R, Dixon B, Drown J et al. (2019) Domestic-wild hybridization to improve aquaculture performance in Chinook salmon. Aquaculture 511:734255
Google Scholar
Smith CC, Snowberg LK, Caporaso JG, Knight R, Bolnick DI (2015) Dietary input of microbes and host genetic variation shape among-population differences in stickleback gut microbiota. ISME J 9(11):2515–2526
Google Scholar
Snijders AM, Langley SA, Kim YM, Brislawn CJ, Noecker C, Zink EM et al. (2016) Influence of early life exposure, host genetics and diet on the mouse gut microbiome and metabolome. Nat Microbiol 2(2):1–8
Google Scholar
Soltani M, Ghosh K, Hoseinifar SH, Kumar V, Lymbery AJ, Roy S et al. (2019) Genus bacillus, promising probiotics in aquaculture: Aquatic animal origin, bio-active components, bioremediation and efficacy in fish and shellfish. Rev Fish Sci Aquac 27(3):331–379
Google Scholar
Spor A, Koren O, Ley R (2011) Unravelling the effects of the environment and host genotype on the gut microbiome. Nat Rev Microbiol 9(4):279–290
Google Scholar
Sullam KE, Rubin BE, Dalton CM, Kilham SS, Flecker AS, Russell JA (2015) Divergence across diet, time and populations rules out parallel evolution in the gut microbiomes of Trinidadian guppies. ISME J 9(7):1508–1522
Google Scholar
Suzuki TA (2017) Links between natural variation in the microbiome and host fitness in wild mammals. Integr Comp Biol 57(4):756–769
Google Scholar
Toews SD, Wellband KW, Dixon B, Heath DD (2019) Variation in juvenile Chinook salmon (Oncorhynchus tshawytscha) transcription profiles among and within eight population crosses from British Columbia, Canada. Mol Ecol 28(8):1890–1903
Google Scholar
Tremaroli V, Bäckhed F (2012) Functional interactions between the gut microbiota and host metabolism. Nature 489(7415):242–249
Google Scholar
Unwin MJ, Quinn TP, Kinnison MT, Boustead NC (2000) Divergence in juvenile growth and life history in two recently colonized and partially isolated chinook salmon populations. J Fish Biol 57(4):943–960
Google Scholar
Vähä JP, Erkinaro J, Niemelä E, Primmer CR (2008) Temporally stable genetic structure and low migration in an Atlantic salmon population complex: implications for conservation and management. Evolut Appl 1(1):137–154
Google Scholar
van Oppen MJ, Oliver JK, Putnam HM, Gates RD (2015) Building coral reef resilience through assisted evolution. Proc Natl Acad Sci 112(8):2307–2313
Google Scholar
Villasante A, Ramírez C, Catalán N, Opazo R, Dantagnan P, Romero J (2019) Effect of dietary carbohydrate-to-protein ratio on gut microbiota in atlantic salmon (Salmo salar). Animals 9(3):89
Google Scholar
Visscher PM, Hill WG, Wray NR (2008) Heritability in the genomics era—concepts and misconceptions. Nat Rev Genet 9(4):255–266
Google Scholar
Waples RS, Teel DJ, Myers JM, Marshall AR (2004) Life‐history divergence in Chinook salmon: historic contingency and parallel evolution. Evolution 58(2):386–403
Google Scholar
Waples RS, Naish KA, Primmer CR (2019) Conservation and Management of Salmon in the Age of Genomics. Annual review of animal biosciences 8.
Webster TMU, Consuegra S, Hitchings M, de Leaniz CG (2018) Interpopulation variation in the Atlantic salmon microbiome reflects environmental and genetic diversity. Appl Environ Microbiol 84(16):e00691–18
Webster TMU, Rodriguez‐Barreto D, Castaldo G, Gough P, Consuegra S, Garcia de Leaniz C (2020) Environmental plasticity and colonisation history in the Atlantic salmon microbiome: a translocation experiment. Mol Ecol Mar 29(5):886–898
Google Scholar
Wickham H (2016) ggplot2: elegant graphics for data analysis. Springer
Google Scholar
Willems A (2014) The family Comamonadaceae. The prokaryotes: Alphaproteobacteria and Betaproteobacteria. The Prokaryotes. Springer, Berlin
Wong S, Rawls JF (2012) Intestinal microbiota composition in fishes is influenced by host ecology and environment. Mol Ecol 21(13):3100–3102
Google Scholar
Wong S, Waldrop T, Summerfelt S, Davidson J, Barrows F, Kenney PB et al. (2013) Aquacultured rainbow trout (Oncorhynchus mykiss) possess a large core intestinal microbiota that is resistant to variation in diet and rearing density. Appl Environ Microbiol 79(16):4974–4984
Google Scholar
Wringe BF, Jeffery NW, Stanley RR, Hamilton LC, Anderson EC, Fleming IA et al. (2018) Extensive hybridization following a large escape of domesticated Atlantic salmon in the Northwest Atlantic. Commun Biol 1(1):1–9
Google Scholar
Wrobel A, Leo JC, Linke D (2019) Overcoming fish defences: the virulence factors of Yersinia ruckeri. Genes 10(9):700
Google Scholar
Wu SG, Tian JY, Gatesoupe FJ, Li WX, Zou H, Yang BJ et al. (2013) Intestinal microbiota of gibel carp (Carassius auratus gibelio) and its origin as revealed by 454 pyrosequencing. World J Microbiol Biotechnol 29(9):1585–1595
Google Scholar
Xiao F, Zhu W, Yu Y et al. (2021) Host development overwhelms environmental dispersal in governing the ecological succession of zebrafish gut microbiota. npj Biofilms Microbiomes 7:5
Google Scholar
Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M et al. (2012) Human gut microbiome viewed across age and geography. Nature 486(7402):222–227
Google Scholar
Ye L, Amberg J, Chapman D, Gaikowski M, Liu WT (2014) Fish gut microbiota analysis differentiates physiology and behavior of invasive Asian carp and indigenous American fish. ISME J 8(3):541–551
Google Scholar
Yeaman S, Otto SP (2011) Establishment and maintenance of adaptive genetic divergence under migration, selection, and drift. Evol: Int J Org Evol 65(7):2123–2129
Google Scholar
Yilmaz P et al. (2014) The SILVA and “all-species living tree project (LTP)” taxonomic frameworks. Nucleic Acids Res 42(D1):D643–D648
Google Scholar