FAO Meeting the sustainable development goals. 2018.
Google Scholar
World population prospects 2019. Available at https://population.un.org/wpp/.
Assefa A, Abunna F. Maintenance of fish health in aquaculture: review of epidemiological approaches for prevention and control of infectious disease of fish: Veterinary Medicine International; 2018. https://www.hindawi.com/journals/vmi/2018/5432497/. Accessed 8 Apr 2020.
Pridgeon J. Major bacterial diseases in aquaculture and their vaccine development. CAB Rev Perspect Agric Vet Sci Nutr Nat Resour. 2012;7(048):1-16. https://doi.org/10.1079/PAVSNNR20127048.
Ventola CL. The antibiotic resistance crisis. Pharm Ther. 2015;40(4):277–83.
Google Scholar
Nayak SK. Role of gastrointestinal microbiota in fish. Aquac Res. 2010;41(11):1553–73. https://doi.org/10.1111/j.1365-2109.2010.02546.x.
Article
Google Scholar
Romero J, Ringø E, Merrifield DL. The gut microbiota of fish. In: Aquaculture nutrition: Wiley; 2014. p. 75–100.
Egerton S, Culloty S, Whooley J, Stanton C, Ross RP. The gut microbiota of marine fish. Front Microbiol. 2018;9:873. https://doi.org/10.3389/fmicb.2018.00873.
de Bruijn I, Liu Y, Wiegertjes GF, Raaijmakers JM. Exploring fish microbial communities to mitigate emerging diseases in aquaculture. FEMS Microbiol Ecol. 2018;94(1):fix161. https://doi.org/10.1093/femsec/fix161.
Article
CAS
Google Scholar
Xiong J-B, Nie L, Chen J. Current understanding on the roles of gut microbiota in fish disease and immunity. Zool Res. 2019;40(2):70–6. https://doi.org/10.24272/j.issn.2095-8137.2018.069.
Article
PubMed
Google Scholar
Tran NT, Zhang J, Xiong F, Wang G-T, Li W-X, Wu S-G. Altered gut microbiota associated with intestinal disease in grass carp (Ctenopharyngodon idellus). World J Microbiol Biotechnol. 2018;34(6):71. https://doi.org/10.1007/s11274-018-2447-2.
Article
CAS
PubMed
Google Scholar
Wang C, Sun G, Li S, Li X, Liu Y. Intestinal microbiota of healthy and unhealthy Atlantic salmon Salmo salar L. in a recirculating aquaculture system. J Oceanol Limnol. 2018;36(2):414–26. https://doi.org/10.1007/s00343-017-6203-5.
Article
CAS
Google Scholar
Rosado D, Xavier R, Severino R, Tavares F, Cable J, Pérez-Losada M. Effects of disease, antibiotic treatment and recovery trajectory on the microbiome of farmed seabass ( Dicentrarchus labrax ). Sci Rep. 2019;9(1):1–11. https://doi.org/10.1038/s41598-019-55314-4.
Article
CAS
Google Scholar
Standen BT, Rawling MD, Davies SJ, Castex M, Foey A, Gioacchini G, et al. Probiotic Pediococcus acidilactici modulates both localised intestinal- and peripheral-immunity in tilapia (Oreochromis niloticus). Fish Shellfish Immunol. 2013;35(4):1097–104. https://doi.org/10.1016/j.fsi.2013.07.018.
Article
CAS
PubMed
Google Scholar
Tarnecki AM, Wafapoor M, Phillips RN, Rhody NR. Benefits of a Bacillus probiotic to larval fish survival and transport stress resistance. Sci Rep. 2019;9(1):1. https://doi.org/10.1038/s41598-019-39316-w.
Article
CAS
Google Scholar
Nguyen TL, et al. Dietary probiotic effect of lactococcus lactis WFLU12 on low-molecular-weight metabolites and growth of olive flounder (Paralichythys olivaceus). Front Microbiol. 2018;9:2059. https://doi.org/10.3389/fmicb.2018.02059.
Article
PubMed
PubMed Central
Google Scholar
Yi Y, Zhang Z, Zhao F, Liu H, Yu L, Zha J, et al. Probiotic potential of Bacillus velezensis JW: antimicrobial activity against fish pathogenic bacteria and immune enhancement effects on Carassius auratus. Fish Shellfish Immunol. 2018;78:322–30. https://doi.org/10.1016/j.fsi.2018.04.055.
Article
CAS
PubMed
Google Scholar
Liu C-H, Wu K, Chu T-W, Wu T-M. Dietary supplementation of probiotic, Bacillus subtilis E20, enhances the growth performance and disease resistance against Vibrio alginolyticus in parrot fish (Oplegnathus fasciatus). Aquac Int. 2018;26(1):63–74. https://doi.org/10.1007/s10499-017-0189-z.
Article
CAS
Google Scholar
Dehler CE, Secombes CJ, Martin SAM. Environmental and physiological factors shape the gut microbiota of Atlantic salmon parr (Salmo salar L.). Aquaculture. 2017;467:149–57. https://doi.org/10.1016/j.aquaculture.2016.07.017.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gajardo K, et al. Alternative protein sources in the diet modulate microbiota and functionality in the distal intestine of Atlantic salmon (Salmo salar). Appl Environ Microbiol. 2017;83(5):1. https://doi.org/10.1128/AEM.02615-16.
Article
Google Scholar
Zhang Z, Li D, Xu W, Tang R, Li L. Microbiome of co-cultured fish exhibits host selection and niche differentiation at the organ scale. Front Microbiol. 2019;10:2576. https://doi.org/10.3389/fmicb.2019.02576.
Article
PubMed
PubMed Central
Google Scholar
Turner S, Pryer KM, Miao VP, Palmer JD. Investigating deep phylogenetic relationships among cyanobacteria and plastids by small subunit rRNA sequence analysis. J Eukaryot Microbiol. 1999;46(4):327–38. https://doi.org/10.1111/j.1550-7408.1999.tb04612.x.
Article
CAS
PubMed
Google Scholar
Leal JF, Neves MGPMS, Santos EBH, Esteves VI. Use of formalin in intensive aquaculture: properties, application and effects on fish and water quality. Rev Aquac. 2018;10(2):281–95. https://doi.org/10.1111/raq.12160.
Article
Google Scholar
Francis-Floyd R. Use of formalin to control fish parasites; 1996.
Google Scholar
Schnell IB, Bohmann K, Gilbert MTP. Tag jumps illuminated – reducing sequence-to-sample misidentifications in metabarcoding studies. Mol Ecol Resour. 2015;15(6):1289–303. https://doi.org/10.1111/1755-0998.12402.
Article
CAS
PubMed
Google Scholar
Schrader C, Schielke A, Ellerbroek L, Johne R. PCR inhibitors – occurrence, properties and removal. J Appl Microbiol. 2012;113(5):1014–26. https://doi.org/10.1111/j.1365-2672.2012.05384.x.
Article
CAS
PubMed
Google Scholar
Yu Y, Lee C, Kim J, Hwang S. Group-specific primer and probe sets to detect methanogenic communities using quantitative real-time polymerase chain reaction. Biotechnol Bioeng. 2005;89(6):670–9. https://doi.org/10.1002/bit.20347.
Article
CAS
PubMed
Google Scholar
Graspeuntner S, Loeper N, Künzel S, Baines JF, Rupp J. Selection of validated hypervariable regions is crucial in 16S-based microbiota studies of the female genital tract. Sci Rep. 2018;8(1):1. https://doi.org/10.1038/s41598-018-27757-8.
Article
CAS
Google Scholar
Teng F, et al. Impact of DNA extraction method and targeted 16S-rRNA hypervariable region on oral microbiota profiling. Sci Rep. 2018;8(1):1. https://doi.org/10.1038/s41598-018-34294-x.
Article
CAS
Google Scholar
DeAngelis MM, Wang DG, Hawkins TL. Solid-phase reversible immobilization for the isolation of PCR products. Nucleic Acids Res. 1995;23(22):4742–3.
Article
CAS
PubMed
PubMed Central
Google Scholar
Carøe C, Bohmann K. Tagsteady: a metabarcoding library preparation protocol to avoid false assignment of sequences to samples. Mol Ecol Resour. 2020. https://doi.org/10.1111/1755-0998.13227.
Andrews S. Babraham bioinformatics - FastQC a quality control tool for high throughput sequence data; 2010. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ (Accessed 20 Apr 2020).
Google Scholar
Schubert M, Lindgreen S, Orlando L. AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Res Notes. 2016;9(1):88. https://doi.org/10.1186/s13104-016-1900-2.
Article
PubMed
PubMed Central
Google Scholar
Zepeda-Mendoza ML, Bohmann K, Carmona Baez A, Gilbert MTP. DAMe: a toolkit for the initial processing of datasets with PCR replicates of double-tagged amplicons for DNA metabarcoding analyses. BMC Res Notes. 2016;9(1):255. https://doi.org/10.1186/s13104-016-2064-9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mercier et al. SUMATRA and SUMACLUST: fast and exact comparison and clustering of sequences; 2013.
Google Scholar
Callahan BJ, McMurdie PJ, Holmes SP. Exact sequence variants should replace operational taxonomic units in marker-gene data analysis. ISME J. 2017;11(12):12. https://doi.org/10.1038/ismej.2017.119.
Article
Google Scholar
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7(5):335–6. https://doi.org/10.1038/nmeth.f.303.
Article
CAS
PubMed
PubMed Central
Google Scholar
Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32(5):1792–7. https://doi.org/10.1093/nar/gkh340.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 2011;28(10):2731–9. https://doi.org/10.1093/molbev/msr121.
Article
CAS
PubMed
PubMed Central
Google Scholar
de Goffau MC, et al. Recognizing the reagent microbiome. Nat Microbiol. 2018;3(8):8. https://doi.org/10.1038/s41564-018-0202-y.
Article
CAS
Google Scholar
Salter SJ, et al. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol. 2014;12(1):87. https://doi.org/10.1186/s12915-014-0087-z.
Article
CAS
PubMed
PubMed Central
Google Scholar
Glassing A, Dowd SE, Galandiuk S, Davis B, Chiodini RJ. Inherent bacterial DNA contamination of extraction and sequencing reagents may affect interpretation of microbiota in low bacterial biomass samples. Gut Pathog. 2016;8(1):24. https://doi.org/10.1186/s13099-016-0103-7.
Article
CAS
PubMed
PubMed Central
Google Scholar
R Core Team and R Foundation for Statistical Computing. R: a language and environment for statistical computing; 2020. Available: https://www.R-project.org/.
Google Scholar
RStudio Team. RStudio: integrated development for R. RStudio, PBC, Boston, MA; 2020. Available: http://www.rstudio.com/.
Google Scholar
Wei T, Simko V. R package “corrplot”: visualization of a correlation matrix (version 0.84). 2017. Available: https://github.com/taiyun/corrplot.
Google Scholar
Dahlberg J, et al. Microbiota data from low biomass milk samples is markedly affected by laboratory and reagent contamination. PLoS ONE. 2019;14(6):e0218257. https://doi.org/10.1371/journal.pone.0218257.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wickham H. ggplot2: elegant graphics for data analysis, 978–3–319-24277-4. Springer-Verlag; 2016. https://ggplot2.tidyverse.org.
Davis NM, Proctor DM, Holmes SP, Relman DA, Callahan BJ. Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data. Microbiome. 2018;6(1):226. https://doi.org/10.1186/s40168-018-0605-2.
Gloor GB, Macklaim JM, Pawlowsky-Glahn V, Egozcue JJ. Microbiome datasets are compositional: and this is not optional. Front Microbiol. 2017;8:2224. https://doi.org/10.3389/fmicb.2017.02224.
Weiss S, et al. Normalization and microbial differential abundance strategies depend upon data characteristics. Microbiome. 2017;5(1):27. https://doi.org/10.1186/s40168-017-0237-y.
Alberdi A, Gilbert MTP. A guide to the application of hill numbers to DNA-based diversity analyses. Mol Ecol Resour. 2019;19(4):804–17. https://doi.org/10.1111/1755-0998.13014.
Article
PubMed
Google Scholar
McMurdie PJ, Holmes S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE. 2013;8(4):e61217. https://doi.org/10.1371/journal.pone.0061217.
Article
CAS
PubMed
PubMed Central
Google Scholar
Oksanen J, Blanchet FG, Friendly M, Kindt R, Legendre P, McGlinn D, Minchin PR, O’Hara RB, Simpson GL, Solymos P, Stevens MHH, Szoecs E, Wagner H. vegan: community ecology package. 2019 R package version 2.5–6., and https://CRAN.R-project.org/package=vegan.
Google Scholar
Warnes GR, Bolker B, Bonebakker L, Gentleman R, Huber W, Liaw A, Lumley T, Maechler M, Magnusson A, Moeller S, Schwartz M, Venables B. gplots: various R programming tools for plotting data, 2020. R package version 3.0.3., [Online]. Available: https://CRAN.R-project.org/package=gplots.
Google Scholar
Neuwirth E. RColorBrewer: ColorBrewer palettes. 2014. Available: https://CRAN.R-project.org/package=RColorBrewer.
Google Scholar
Kassambara A. ggpubr: “ggplot2” based publication ready plots; 2020. Available: https://CRAN.R-project.org/package=ggpubr.
Google Scholar
Barnham C, Baxter A. Condition factor, K, for salmonid fish; 2003. p. 3.
Google Scholar
Yoon S-H, Ha SM, Kwon S, Lim J, Kim Y, Seo H, et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol. 2017;67(5):1613–7. https://doi.org/10.1099/ijsem.0.001755.
Article
CAS
PubMed
PubMed Central
Google Scholar
Avendaño-Herrera R, Toranzo AE, Magariños B. Tenacibaculosis infection in marine fish caused by Tenacibaculum maritimum: a review. Dis Aquat Org. 2006;71(3):255–66. https://doi.org/10.3354/dao071255.
Article
Google Scholar
Pérez-Pascual D, et al. The complete genome sequence of the fish pathogen Tenacibaculum maritimum provides insights into virulence mechanisms. Front Microbiol. 2017;8:1542. https://doi.org/10.3389/fmicb.2017.01542.
Småge SB, Brevik ØJ, Duesund H, Ottem KF, Watanabe K, Nylund A. Tenacibaculum finnmarkense sp. nov., a fish pathogenic bacterium of the family Flavobacteriaceae isolated from Atlantic salmon. Antonie Van Leeuwenhoek. 2016;109(2):273–85. https://doi.org/10.1007/s10482-015-0630-0.
Article
PubMed
Google Scholar
Avendaño-Herrera R, Irgang R, Sandoval C, Moreno-Lira P, Houel A, Duchaud E, et al. Isolation, characterization and virulence potential of Tenacibaculum dicentrarchi in salmonid cultures in Chile. Transbound Emerg Dis. 2016;63(2):121–6. https://doi.org/10.1111/tbed.12464.
Article
CAS
PubMed
Google Scholar
Grothusen H, et al. First complete genome sequence of Tenacibaculum dicentrarchi, an emerging bacterial pathogen of salmonids. Genome Announc. 2016;4(1):e01756–15. https://doi.org/10.1128/genomeA.01756-15.
Klakegg Ø, Abayneh T, Fauske AK, Fülberth M, Sørum H. An outbreak of acute disease and mortality in Atlantic salmon (Salmo salar) post-smolts in Norway caused by Tenacibaculum dicentrarchi. J Fish Dis. 2019;42(6):789–807. https://doi.org/10.1111/jfd.12982.
Article
CAS
PubMed
Google Scholar
Borrego JJ, et al. Vibrio tapetis sp. nov., the causative agent of the brown ring disease affecting cultured clams. Int J Syst Evol Microbiol. 1996;46(2):480–4. https://doi.org/10.1099/00207713-46-2-480.
Article
CAS
Google Scholar
Reid HI, Duncan HL, Laidler LA, Hunter D, Birkbeck TH. Isolation of Vibrio tapetis from cultivated Atlantic halibut (Hippoglossus hippoglossus L.). Aquaculture. 2003;221(1):65–74. https://doi.org/10.1016/S0044-8486(03)00060-7.
Article
Google Scholar
Jensen S, Samuelsen OB, Andersen K, Torkildsen L, Lambert C, Choquet G, et al. Characterization of strains of Vibrio splendidus and V. tapetis isolated from corkwing wrasse Symphodus melops suffering vibriosis. Dis Aquat Org. 2003;53(1):25–31. https://doi.org/10.3354/dao053025.
Article
Google Scholar
Declercq AM, Chiers K, Soetaert M, Lasa A, Romalde JL, Polet H, et al. Vibrio tapetis isolated from vesicular skin lesions in Dover sole Solea solea. Dis Aquat Org. 2015;115(1):81–6. https://doi.org/10.3354/dao02880.
Article
CAS
Google Scholar
Bergh Ø, Samuelsen OB. Susceptibility of corkwing wrasse Symphodus melops, goldsinny wrasse Ctenolabrus rupestis, and Atlantic salmon Salmo salar smolt, to experimental challenge with Vibrio tapetis and Vibrio splendidus isolated from corkwing wrasse. Aquac Int. 2007;15(1):11–8. https://doi.org/10.1007/s10499-006-9061-2.
Article
Google Scholar
Urbanczyk H, Ast JC, Higgins MJ, Carson J, Dunlap PV. Reclassification of Vibrio fischeri, Vibrio logei, Vibrio salmonicida and Vibrio wodanis as Aliivibrio fischeri gen. nov., comb. nov., Aliivibrio logei comb. nov., Aliivibrio salmonicida comb. nov. and Aliivibrio wodanis comb. nov. Int J Syst Evol Microbiol. 2007;57(12):2823–9. https://doi.org/10.1099/ijs.0.65081-0.
Article
CAS
PubMed
Google Scholar
Kashulin A, Seredkina N, Sørum H. Cold-water vibriosis. The current status of knowledge. J Fish Dis. 2017;40(1):119–26. https://doi.org/10.1111/jfd.12465.
Article
CAS
PubMed
Google Scholar
Bano N, Smith AD, Bennett W, Vasquez L, Hollibaugh JT. Dominance of mycoplasma in the guts of the long-jawed Mudsucker, Gillichthys mirabilis, from five California salt marshes. Environ Microbiol. 2007;9(10):2636–41. https://doi.org/10.1111/j.1462-2920.2007.01381.x.
Article
CAS
PubMed
Google Scholar
Kim D-H, Brunt J, Austin B. Microbial diversity of intestinal contents and mucus in rainbow trout (Oncorhynchus mykiss). J Appl Microbiol. 2007;102(6):1654–64. https://doi.org/10.1111/j.1365-2672.2006.03185.x.
Article
CAS
PubMed
Google Scholar
Tamminen M, Karkman A, Corander J, Paulin L, Virta M. Differences in bacterial community composition in Baltic Sea sediment in response to fish farming. Aquaculture. 2011;313(1):15–23. https://doi.org/10.1016/j.aquaculture.2011.01.020.
Article
Google Scholar
Green TJ, Smullen R, Barnes AC. Dietary soybean protein concentrate-induced intestinal disorder in marine farmed Atlantic salmon, Salmo salar is associated with alterations in gut microbiota. Vet Microbiol. 2013;166(1–2):286–92. https://doi.org/10.1016/j.vetmic.2013.05.009.
Article
CAS
PubMed
Google Scholar
Xing M, Hou Z, Yuan J, Liu Y, Qu Y, Liu B. Taxonomic and functional metagenomic profiling of gastrointestinal tract microbiome of the farmed adult turbot (Scophthalmus maximus). FEMS Microbiol Ecol. 2013;86(3):432–43. https://doi.org/10.1111/1574-6941.12174.
Article
CAS
PubMed
Google Scholar
Pizarro-Cerdá J, Cossart P. Bacterial adhesion and entry into host cells. Cell. 2006;124(4):715–27. https://doi.org/10.1016/j.cell.2006.02.012.
Article
CAS
PubMed
Google Scholar
Lokesh J, Kiron V. Transition from freshwater to seawater reshapes the skin-associated microbiota of Atlantic salmon. Sci Rep. 2016;6(1):1. https://doi.org/10.1038/srep19707.
Article
CAS
Google Scholar
Schmidt VT, Smith KF, Melvin DW, Amaral-Zettler LA. Community assembly of a euryhaline fish microbiome during salinity acclimation. Mol Ecol. 2015;24(10):2537–50. https://doi.org/10.1111/mec.13177.
Article
PubMed
Google Scholar
Zhang M, Sun Y, Liu Y, Qiao F, Chen L, Liu WT, et al. Response of gut microbiota to salinity change in two euryhaline aquatic animals with reverse salinity preference. Aquaculture. 2016;454:72–80. https://doi.org/10.1016/j.aquaculture.2015.12.014.
Article
CAS
Google Scholar
Zhao R, Symonds JE, Walker SP, Steiner K, Carter CG, Bowman JP, et al. Salinity and fish age affect the gut microbiota of farmed Chinook salmon (Oncorhynchus tshawytscha). Aquaculture. 2020;528:735539. https://doi.org/10.1016/j.aquaculture.2020.735539.
Article
CAS
Google Scholar
Fogarty C, Burgess CM, Cotter PD, Cabrera-Rubio R, Whyte P, Smyth C, et al. Diversity and composition of the gut microbiota of Atlantic salmon (Salmo salar) farmed in Irish waters. J Appl Microbiol. 2019;127(3):648–57. https://doi.org/10.1111/jam.14291.
Article
CAS
PubMed
Google Scholar
Webster TMU, Rodriguez-Barreto D, Castaldo G, Gough P, Consuegra S, de Leaniz CG. Environmental plasticity and colonisation history in the Atlantic salmon microbiome: a translocation experiment. Mol Ecol. 2020;29(5):886–98. https://doi.org/10.1111/mec.15369.
Article
Google Scholar
Heys C, et al. Neutral processes dominate microbial community assembly in atlantic salmon, Salmo salar. Appl Environ Microbiol. 2020;86(8):e02283–19, /aem/86/8/AEM.02283–19.atom. https://doi.org/10.1128/AEM.02283-19.
Article
CAS
PubMed
PubMed Central
Google Scholar
Llewellyn MS, et al. The biogeography of the atlantic salmon ( Salmo salar ) gut microbiome. ISME J. 2016;10(5):5. https://doi.org/10.1038/ismej.2015.189.
Article
Google Scholar
Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, et al. Human gut microbiome viewed across age and geography. Nature. 2012;486(7402):222–7. https://doi.org/10.1038/nature11053.
Article
CAS
PubMed
PubMed Central
Google Scholar
Karlsen C, Ottem KF, Brevik ØJ, Davey M, Sørum H, Winther-Larsen HC. The environmental and host-associated bacterial microbiota of Arctic seawater-farmed Atlantic salmon with ulcerative disorders. J Fish Dis. 2017;40(11):1645–63. https://doi.org/10.1111/jfd.12632.
Article
CAS
PubMed
Google Scholar
Gupta RS, Sawnani S, Adeolu M, Alnajar S, Oren A. Phylogenetic framework for the phylum Tenericutes based on genome sequence data: proposal for the creation of a new order Mycoplasmoidales Ord. Nov., containing two new families Mycoplasmoidaceae fam. Nov. and Metamycoplasmataceae fam. Nov. harbouring Eperythrozoon, Ureaplasma and five novel genera. Antonie Van Leeuwenhoek. 2018;111(9):1583–630. https://doi.org/10.1007/s10482-018-1047-3.
Article
PubMed
Google Scholar
Holben WE, Williams P, Saarinen M, Särkilahti LK, Apajalahti JHA. Phylogenetic analysis of intestinal microflora indicates a novel mycoplasma phylotype in farmed and wild salmon. Microb Ecol. 2002;44(2):175–85. https://doi.org/10.1007/s00248-002-1011-6.
Article
CAS
PubMed
Google Scholar
Zarkasi KZ, Abell GCJ, Taylor RS, Neuman C, Hatje E, Tamplin ML, et al. Pyrosequencing-based characterization of gastrointestinal bacteria of Atlantic salmon (Salmo salar L.) within a commercial mariculture system. J Appl Microbiol. 2014;117(1):18–27. https://doi.org/10.1111/jam.12514.
Article
CAS
PubMed
Google Scholar
Zarkasi KZ, Taylor RS, Abell GCJ, Tamplin ML, Glencross BD, Bowman JP. Atlantic Salmon (Salmo salar L.) gastrointestinal microbial community dynamics in relation to digesta properties and diet. Microb Ecol. 2016;71(3):589–603. https://doi.org/10.1007/s00248-015-0728-y.
Article
CAS
PubMed
Google Scholar
Ciric M, Waite D, Draper J, Jones JB. Characterization of mid-intestinal microbiota of farmed Chinook salmon using 16S rRNA gene metabarcoding. Arch Biol Sci. 2019;71(4):4.
Article
Google Scholar
Brown RM, Wiens GD, Salinas I. Analysis of the gut and gill microbiome of resistant and susceptible lines of rainbow trout (Oncorhynchus mykiss). Fish Shellfish Immunol. 2019;86:497–506. https://doi.org/10.1016/j.fsi.2018.11.079.
Article
CAS
PubMed
Google Scholar
Lowrey L, Woodhams DC, Tacchi L, Salinas I. Topographical mapping of the rainbow trout (Oncorhynchus mykiss) microbiome reveals a diverse bacterial community with antifungal properties in the skin. Appl Environ Microbiol. 2015;81(19):6915–25. https://doi.org/10.1128/AEM.01826-15.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lyons PP, Turnbull JF, Dawson KA, Crumlish M. Phylogenetic and functional characterization of the distal intestinal microbiome of rainbow trout Oncorhynchus mykiss from both farm and aquarium settings. J Appl Microbiol. 2017;122(2):347–63. https://doi.org/10.1111/jam.13347.
Article
CAS
PubMed
Google Scholar
Lyons PP, Turnbull JF, Dawson KA, Crumlish M. Effects of low-level dietary microalgae supplementation on the distal intestinal microbiome of farmed rainbow trout Oncorhynchus mykiss (Walbaum). Aquac Res. 2017;48(5):2438–52. https://doi.org/10.1111/are.13080.
Article
CAS
Google Scholar
Rimoldi S, Gini E, Iannini F, Gasco L, Terova G. The effects of dietary insect meal from Hermetia illucens prepupae on autochthonous gut microbiota of rainbow trout (Oncorhynchus mykiss). Anim Open Access J MDPI. 2019;9(4):143. https://doi.org/10.3390/ani9040143.
Minich JJ, et al. Microbial ecology of atlantic salmon (Salmo salar) hatcheries: impacts of the built environment on fish mucosal microbiota. Appl Environ Microbiol. 2020;86(12):e00411-20. https://doi.org/10.1128/AEM.00411-20.
Rasmussen JA, et al. Genome-resolved metagenomics suggests a mutualistic relationship between Mycoplasma and salmonid hosts. 2021, PREPRINT (Version 1) available at Research Square https://doi.org/10.21203/rs.3.rs-269923/v1
Webster TMU, Consuegra S, Hitchings M, de Leaniz CG. Interpopulation variation in the atlantic salmon microbiome reflects environmental and genetic diversity. Appl Environ Microbiol. 2018;84(16):1-14. https://doi.org/10.1128/AEM.00691-18.
Legrand TPRA, Catalano SR, Wos-Oxley ML, Wynne JW, Weyrich LS, Oxley APA. Antibiotic-induced alterations and repopulation dynamics of yellowtail kingfish microbiota. Anim Microbiome. 2020;2(1):26. https://doi.org/10.1186/s42523-020-00046-4.
Article
PubMed
PubMed Central
Google Scholar
Legrand TPRA, Wynne JW, Weyrich LS, Oxley APA. Investigating both mucosal immunity and microbiota in response to gut enteritis in yellowtail kingfish. Microorganisms. 2020;8(9):9. https://doi.org/10.3390/microorganisms8091267.
Article
CAS
Google Scholar
Gaulke CA, et al. A longitudinal assessment of host-microbe-parasite interactions resolves the zebrafish gut microbiome’s link to Pseudocapillaria tomentosa infection and pathology. Microbiome. 2019;7(1):10. https://doi.org/10.1186/s40168-019-0622-9.
Article
PubMed
PubMed Central
Google Scholar
Anslan S, Li H, Künzel S, Vences M. Microbiomes from feces vs. gut in aquatic vertebrates: distinct community compositions between substrates and preservation methods. Microbiology. 2019. https://doi.org/10.1101/651612.