Journal of Oceanology and Limnology

, Volume 36, Issue 2, pp 414–426 | Cite as

Intestinal microbiota of healthy and unhealthy Atlantic salmon Salmo salar L. in a recirculating aquaculture system

  • Chun Wang (王纯)
  • Guoxiang Sun (孙国祥)
  • Shuangshuang Li (李双双)
  • Xian Li (李贤)
  • Ying Liu (刘鹰)Email author


The present study sampled the intestinal content of healthy and unhealthy Atlantic salmon (Salmo salar L.), the ambient water of unhealthy fish, and the biofilter material in the recirculating aquaculture system (RAS) to understand differences in the intestinal microbiota. The V4–V5 regions of the prokaryotic 16S rRNA genes in the samples were analyzed by MiSeq high-throughput sequencing. The fish were adults with no differences in body length or weight. Representative members of the intestinal microbiota were identified. The intestinal microbiota of the healthy fish included Proteobacteria (44.33%), Actinobacteria (17.89%), Bacteroidetes (15.25%), and Firmicutes (9.11%), among which the families Micrococcaceae and Oxalobacteraceae and genera Sphingomonas, Streptomyces, Pedobacter, Janthinobacterium, Burkholderia, and Balneimonas were most abundant. Proteobacteria (70.46%), Bacteroidetes (7.59%), and Firmicutes (7.55%) dominated the microbiota of unhealthy fish, and Chloroflexi (2.71%), and Aliivibrio and Vibrio as well as genera in the family Aeromonadaceae were most strongly represented. Overall, the intestinal hindgut microbiota differed between healthy and unhealthy fish. This study offers a useful tool for monitoring the health status of fish and for screening the utility of probiotics by studying the intestinal microbiota.


intestinal microbiota health status Atlantic salmon (Salmo salar L.) recirculating aquaculture system high-throughput pyrosequencing 


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  1. Backhed F, Ding H, Wang T, Hooper L V, Koh G Y, Nagy A, Semenkovich C F, Gordon J I. 2004. The gut microbiota as an environmental factor that regulates fat storage. Proc. Natl. Acad. Sci. U. S. A., 101 (44): 15718–15723.CrossRefGoogle Scholar
  2. Bakke-McKellep A M, Penn M H, Salas P M, Refstie S, Sperstad S, Landsverk T, Ringø E, Krogdahl Å. 2007. Effects of dietary soyabean meal, inulin and oxytetracycline on intestinal microbiota and epithelial cell stress, apoptosis and proliferation in the teleost Atlantic salmon (Salmo salar L.). Brit. J. Nutr., 97 (4): 699–713.CrossRefGoogle Scholar
  3. Balcázar J L, Vendrell D, de Blas I, Ruiz-Zarzuela I, Muzquiz J L, Girones O. 2008. Characterization of probiotic properties of lactic acid bacteria isolated from intestinal microbiota of fish. Aquaculture, 278 (1-4): 188–191.CrossRefGoogle Scholar
  4. Bik E M, Eckburg P B, Gill S R, Nelson K E, Purdom E A, Francois F, Perez-Perez G, Blaser M J, Relman D A. 2006. Molecular analysis of the bacterial microbiota in the human stomach. Proc. Natl. Acad. Sci. U. S. A., 103 (3): 732–737.CrossRefGoogle Scholar
  5. Blumberg R, Powrie F. 2012. Microbiota, disease, and back to health: a metastable journey. Sci. Transl. Med., 4 (137): 137rv7.CrossRefGoogle Scholar
  6. Caporaso J G, Kuczynski J, Stombaugh J, Bittinger K, Bushman F D, Costello E K, Fierer N, Peña A G, Goodrich J K, Gordon J I, Huttley G A, Kelley S T, Knights D, Koenig J E, Ley R E, Lozupone C A, McDonald D, McDonald B D, Pirrung M, Reeder J, Sevinsky J R, Turnbaugh P J, Walters W A, Widmann J, Yatsunenko T, Zaneveld J, Knight R. 2010. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods., 7 (5): 335–336.CrossRefGoogle Scholar
  7. Claesson M J, Jeffery I B, Conde S, Power S E, O’Connor E M, Cusack S, Harris H M B, Coakley M, Lakshminarayanan B, O’Sullivan O, Fitzgerald G F, Deane J, O’Connor M, Harnedy N, O’Connor K, O’Mahony D, van Sinderen D, Wallace M, Brennan L, Stanton C, Marchesi J R, Fitzgerald A P, Shanahan F, Hill C, Ross R P, O’Toole P W. 2012. Gut microbiota composition correlates with diet and health in the elderly. Nature, 488 (7410): 178–184.CrossRefGoogle Scholar
  8. Cole J R. 2003. The ribosomal database project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic. Acids. Res., 31 (1): 442–443.CrossRefGoogle Scholar
  9. Das S, Ward L R, Burke C. 2010. Screening of marine Streptomyces spp. for potential use as probiotics in aquaculture. Aquaculture, 305 (1-4): 32–41.CrossRefGoogle Scholar
  10. Defoirdt T, Boon N, Sorgeloos P, Verstraete W, Bossier P. 2007. Alternatives to antibiotics to control bacterial infections: luminescent vibriosis in aquaculture as an example. Trends. Biotechnol., 25 (10): 472–479.CrossRefGoogle Scholar
  11. Desai A R, Links M G, Collins S A, Mansfield G S, Drew M D, Van Kessel A G, Hill J E. 2012. Effects of plant-based diets on the distal gut microbiome of rainbow trout (Oncorhynchus mykiss). Aquaculture, 350-353: 134–142.CrossRefGoogle Scholar
  12. DeSantis T Z, Hugenholtz P, Larsen N, Rojas M, Brodie E L, Keller K, Huber T, Dalevi D, Hu P, Andersen G L. 2006. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl. Environ. Microbiol., 72 (7): 5069–5072.CrossRefGoogle Scholar
  13. Dharmaraj S. 2011. Antagonistic potential of marine actinobacteria against fish and shellfish pathogens. Turk. J. Bio l., 35 (3): 303–311.Google Scholar
  14. Donskey C J. 2004. The role of the intestinal tract as a reservoir and source for transmission of nosocomial pathogens. Clin. Infect. Dis., 39 (2): 219–226.CrossRefGoogle Scholar
  15. Du Y S, Yi M M, Xiao P, Meng L J, Li X, Sun G X, Liu Y. 2015. The impact of Aeromonas salmonicida infection on innate immune parameters of Atlantic salmon (Salmo salar L). Fish. Shellfish. Immun., 44 (1): 307–315.CrossRefGoogle Scholar
  16. Edgar R C, Haas B J, Clemente J C, Quince C, Knight R. 2011. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics, 27 (16): 2194–2200.CrossRefGoogle Scholar
  17. Ewart K V, Belanger J C, Williams J, Karakach T, Penny S, Tsoi S C M, Richards R C, Douglas S E. 2005. Identification of genes differentially expressed in Atlantic salmon (Salmo salar) in response to infection by Aeromonas salmonicida using cDNA microarray technology. Dev. Comp. Immunol., 29 (4): 333–347.CrossRefGoogle Scholar
  18. Gill N, Wlodarska M, Finlay B. 2011. Roadblocks in the gut: barriers to enteric infection. Cell. Microbiol., 13 (5): 660–669.CrossRefGoogle Scholar
  19. Gill S R, Pop M, DeBoy R T, Eckburg P B, Turnbaugh P J, Samuel B S, Gordon J I, Relman D A, Fraser-Liggett C M, Nelson K E. 2006. Metagenomic analysis of the human distal gut microbiome. Science, 312 (5778): 1355–1359.CrossRefGoogle Scholar
  20. Giongo A, Gano K A, Crabb D B, Mukherjee N, Novelo L L, Casella G, Drew J C, Ilonen J, Knip M, Hyöty H, Veijola R, Simell T, Simell O, Neu J, Wasserfall C H, Schatz D, Atkinson M A, Triplett E W. 2011. Toward defining the autoimmune microbiome for type 1 diabetes. ISME J, 5 (1): 82–91.CrossRefGoogle Scholar
  21. Gómez G D, Balcázar J L. 2008. A review on the interactions between gut microbiota and innate immunity of fish. FEMS Immunol. Med. Microbiol., 52 (2): 145–154.CrossRefGoogle Scholar
  22. Goodfellow M, Williams S T. 1983. Ecology of actinomycetes. Annu. Rev. Microbiol., 37: 189–216.CrossRefGoogle Scholar
  23. Gustafson C E, Thomas C J, Trust T J. 1992. Detection of Aeromonas salmonicida from fish by using polymerase chain reaction amplification of the virulence surface array protein gene. Appl. Environ. Microb iol., 58 (12): 3816–3825.Google Scholar
  24. Han S F, Liu Y C, Zhou Z G, He S X, Cao Y N, Shi P, Yao B, Ring Ö E. 2010. Analysis of bacterial diversity in the intestine of grass carp (Ctenopharyngodon idellus) based on 16S rDNA gene sequences. Aquac. Res., 42 (1): 47–56.CrossRefGoogle Scholar
  25. Hansen G H, Olafsen J A. 1999. Bacterial interactions in early life stages of marine cold water fish. Microb. Ecol., 38 (1): 1–26.CrossRefGoogle Scholar
  26. Hooper L V, Littman D R, Macpherson A J. 2012. Interactions between the microbiota and the immune system. Science, 336 (6086): 1268–1273.CrossRefGoogle Scholar
  27. Hughes J B, Hellmann J J, Ricketts T H, Bohannan B J M. 2001. Counting the uncountable: statistical approaches to estimating microbial diversity. Appl. Environ. Microb iol., 67 (10): 4399–4406.CrossRefGoogle Scholar
  28. Janda J M, Abbott S L. 2010. The genus aeromonas: taxonomy, pathogenicity, and infection. Clin. Microbiol. Rev., 23 (1): 35–73.CrossRefGoogle Scholar
  29. Kim D H, Brunt J, Austin B. 2007. Microbial diversity of intestinal contents and mucus in rainbow trout (Oncorhynchus mykiss). J. Appl. Microbiol., 102 (6): 1654–1664.CrossRefGoogle Scholar
  30. Koskinen R, Ali-Vehmas T, Kämpfer P, Laurikkala M, Tsitko I, Kostyal E, Atroshi F, Salkinoja-Salonen M. 2000. Characterization of Sphingomonas isolates from Finnish and Swedish drinking water distribution systems. J. Appl. Microbiol., 89 (4): 687–696.CrossRefGoogle Scholar
  31. Levine J M, D'Antonio C M. 1999. Elton revisited: a review of evidence linking diversity and invasibility. Oikos, 87 (1): 15–26.CrossRefGoogle Scholar
  32. Li X M, Yu Y H, Feng W S, Yan Q Y, Gong Y C. 2012. Host species as a strong determinant of the intestinal microbiota of fish larvae. J. Microbiol., 50 (1): 29–37.CrossRefGoogle Scholar
  33. Li X M, Zhu Y J, Yan Q Y, Ringø E, Yang D G. 2014. Do the intestinal microbiotas differ between paddlefish (Polyodon spathala) and bighead carp (Aristichthys nobilis) reared in the same pond?. J. Appl. Microbiol., 117 (5): 1245–1252.CrossRefGoogle Scholar
  34. Llewellyn M S, McGinnity P, Dionne M, Letourneau J, Thonier F, Carvalho G R, Creer S, Derome N. 2015. The biogeography of the atlantic salmon (Salmo salar) gut microbiome. ISME J., 10 (5): 1280–1284.CrossRefGoogle Scholar
  35. Manichanh C, Borruel N, Casellas F, Guarner F. 2012. The gut microbiota in IBD. Nat. Rev. Gastroenterol. Hepatol., 9 (10): 599–608.CrossRefGoogle Scholar
  36. Navarrete P, Magne F, Mardones P, Riveros M, Opazo R, Suau A, Pochart P, Romero J. 2010. Molecular analysis of intestinal microbiota of rainbow trout (Oncorhynchus mykiss). FEMS Microbiol. Ecol., 71 (1): 148–156.CrossRefGoogle Scholar
  37. Nelson A M, Walk S T, Taube S, Taniuchi M, Houpt E R, Wobus C E, Young V B. 2012. Disruption of the human gut microbiota following Norovirus infection. PLoS One, 7 (10): e48224.CrossRefGoogle Scholar
  38. Ni J J, Yan Q Y, Yu Y H, Zhang T L. 2014. Factors influencing the grass carp gut microbiome and its effect on metabolism. FEMS Microbiol. Ecol., 87 (3): 704–714.CrossRefGoogle Scholar
  39. Ni J J, Yu Y H, Zhang T L, Gao L. 2012. Comparison of intestinal bacterial communities in grass carp, Ctenopharyngodon idellus, from two different habitats. Chin. J. Oceanol. Limn ol., 30 (5): 757–765.CrossRefGoogle Scholar
  40. Nicholson J K, Holmes E, Kinross J, Burcelin R, Gibson G, Jia W, Pettersson S. 2012. Host-gut microbiota metabolic interactions. Science, 336 (6086): 1262–1267.CrossRefGoogle Scholar
  41. O'Hara A M, Shanahan F. 2006. The gut flora as a forgotten organ. EMBO Rep., 7 (7): 688–693.CrossRefGoogle Scholar
  42. Penn K, Jenkins C, Nett M, Udwary D W, Gontang E A, McGlinchey R P, Foster B, Lapidus A, Podell S, Allen E E, Moore B S, Jensen P R. 2009. Genomic islands link secondary metabolism to functional adaptation in marine Actinobacteria. ISME J., 3 (10): 1193–1203.CrossRefGoogle Scholar
  43. Peter H, Beier S, Bertilsson S, Lindström E S, Langenheder S, Tranvik L J. 2011. Function-specific response to depletion of microbial diversity. ISME J., 5 (2): 351–361.CrossRefGoogle Scholar
  44. Rawls J F, Samuel B S, Gordon J I. 2004. Gnotobiotic zebrafish reveal evolutionarily conserved responses to the gut microbiota. Proc. Natl. Acad. Sci. U. S. A., 101 (13): 4596–4601.CrossRefGoogle Scholar
  45. Ray A K, Ghosh K, Ringø E. 2012. Enzyme-producing bacteria isolated from fish gut: a review. Aquacult. Nutr., 18 (5): 465–492.CrossRefGoogle Scholar
  46. Reveco F E, Øverland M, Romarheim O H, Mydland L T. 2014. Intestinal bacterial community structure differs between healthy and inflamed intestines in Atlantic salmon (Salmo salar L.). Aquaculture, 420-421: 262–269.CrossRefGoogle Scholar
  47. Ringø E, Birkbeck T H. 1999. Intestinal microflora of fish larvae and fry. Aquac. Res., 30 (2): 73–93.CrossRefGoogle Scholar
  48. Romero J, Navarrete P. 2006. 16S rDNA-based analysis of dominant bacterial populations associated with early life stages of coho salmon (Oncorhynchus kisutch). Microb. Ecol., 51 (4): 422–430.CrossRefGoogle Scholar
  49. Round J L, Mazmanian S K. 2009. The gut microbiota shapes intestinal immune responses during health and disease. Nat. Rev. Immunol., 9 (5): 313–323.CrossRefGoogle Scholar
  50. Shin N R, Whon T W, Bae J W. 2015. Proteobacteria: microbial signature of dysbiosis in gut microbiota. Trends Biotechnol., 33 (9): 496–503.CrossRefGoogle Scholar
  51. Sommer F, Bäckhed F. 2013. The gut microbiota—masters of host development and physiology. Nat. Rev. Microbiol., 11 (4): 227–238.CrossRefGoogle Scholar
  52. Sullam K E, Essinger S D, Lozupone C A, O'Connor M P, Rosen G L, Knight R, Kilham S, Russell J A. 2012. Environmental and ecological factors that shape the gut bacterial communities of fish: a meta-analysis. Mol. Ecol., 21 (13): 3363–3378.CrossRefGoogle Scholar
  53. Velmurugan S, John S T, Nagaraj D S, Ashine T A, Kumaran S, Pugazhvendan S. 2015. Isolation of actinomycetes from shrimp culture pond and antagonistic to pathogenic Vibrio spp. and WSSV. Int. J. Curr. Microbiol. App. Sci., 4 (7): 82–92.Google Scholar
  54. Verschuere L, Rombaut G, Sorgeloos P, Verstraete W. 2000. Probiotic bacteria as biological control agents in aquaculture. Microbiol. Mol. Biol. R., 64 (4): 655–671.CrossRefGoogle Scholar
  55. Wang L M, Zhao B, Li F S, Xu K, Ma C Q, Tao F, Li Q G, Xu P. 2011. Highly efficient production of D-lactate by Sporolactobacillus sp. CASD with simultaneous enzymatic hydrolysis of peanut meal. Appl. Microbiol. Biot., 89 (4): 1009–1017.CrossRefGoogle Scholar
  56. Wang T T, Cai G X, Qiu Y P, Fei N, Zhang M H, Pang X Y, Jia W, Cai S J, Zhao L P. 2012. Structural segregation of gut microbiota between colorectal cancer patients and healthy volunteers. ISME J., 6 (2): 320–329.CrossRefGoogle Scholar
  57. Willing B P, Russell S L, Finlay B. 2011. Shifting the balance: antibiotic effects on host-microbiota mutualism. Nat. Rev. Microbiol., 9 (4): 233–243.CrossRefGoogle Scholar
  58. Wolfensohn S, Lloyd M. 2008. Handbook of Laboratory Animal Management and Welfare. 3 rd edn. John Wiley & Sons, United Kingdom.Google Scholar
  59. Wu S G, Wang G T, Angert E R, Wang W W, Li W X, Zou H. 2012. Composition, diversity, and origin of the bacterial community in grass carp intestine. PLoS One, 7 (2): e30440.CrossRefGoogle Scholar
  60. Yan Q Y, van der Gast C J, Yu Y H. 2012. Bacterial community assembly and turnover within the intestines of developing zebrafish. PLoS One, 7 (1): e30603.CrossRefGoogle Scholar
  61. Zheng Y F, Yu M, Liu Y, Su Y, Xu T, Yu M C, Zhang X H. 2016. Comparison of cultivable bacterial communities associated with Pacific white shrimp (Litopenaeus vannamei) larvae at different health statuses and growth stages. Aquaculture, 451: 163–169.CrossRefGoogle Scholar

Copyright information

© Chinese Society for Oceanology and Limnology, Science Press and Springer-Verlag GmbH Germany, part of Springer Nature 2017

Authors and Affiliations

  • Chun Wang (王纯)
    • 1
    • 2
  • Guoxiang Sun (孙国祥)
    • 1
  • Shuangshuang Li (李双双)
    • 3
  • Xian Li (李贤)
    • 1
  • Ying Liu (刘鹰)
    • 1
    Email author
  1. 1.Institute of OceanologyChinese Academy of SciencesQingdaoChina
  2. 2.University of Chinese Academy of SciencesBeijingChina
  3. 3.College of Energy and Environmental EngineeringHebei University of EngineeringHandanChina

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