Atlantic Salmon (Salmo salar L., 1758) Gut Microbiota Profile Correlates with Flesh Pigmentation: Cause or Effect?


In Tasmania (Australia), during the marine phase, it has been observed that flesh pigmentation significantly drops in summer, possibly due to high water temperatures (> 20 °C). Although this deleterious effect of summer temperatures has been ascertained, there is a lack of knowledge of the actual mechanisms behind the impaired uptake and/or loss of pigments in Atlantic salmon in a challenging environment. Since the microbial community in the fish intestine significantly changes in relation to the variations of water temperature, this study was conducted to assess how the gut microbiota profile also correlates with the flesh color during temperature fluctuation. We sampled 68 fish at three time points covering the end of summer to winter at a marine farm in Tasmania, Australia. Flesh color was examined in two ways: the average color throughout and the evenness of the color between different areas of the fillet. Using 16S rRNA sequencing of the v3–v4 region, we determined that water temperature corresponded to changes in the gut microbiome both with alpha diversity (Kruskal-Wallis tests P = 0.05) and beta diversity indices (PERMANOVA P = 0.001). Also, there was a significant correlation between the microbiota and the color of the fillet (PERMANOVA P = 0.016). There was a high abundance of Pseudoalteromonadaceae, Enterobacteriaceae, Microbacteriaceae, and Vibrionaceae in the pale individuals. Conversely, carotenoid-synthesizing bacteria families (Bacillaceae, Mycoplasmataceae, Pseudomonas, Phyllobacteriaceae, and Comamonadaceae) were found in higher abundance in individuals with darker flesh color.

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Availability of Data and Material

The metadata file, rarefied, and unrarefied OTU tables, and sequences files used in this study are undergoing the process of deposition in the European Bioinformatics Institute (EBI) repository. The metadata file can be found in Supplemental Material S1. The full records of core diversities and differentiation analysis are included as Supplemental Material S2 and S3, respectively, which are also undergoing the process of deposition in EBI as qzv and qza file type.













Kyoto Encyclopedia of Genes and Genomes


KEGG Orthology


Linear Discriminant Analysis


linear discriminant analysis effect size




Operational Taxonomic Unit




Phylogenetic Investigation of Communities by Reconstruction of Unobserved States


Quantitative Insights into Microbial Ecology




  1. Aas GH, Bjerkeng B, Storebakken T, Ruyter B (1999) Blood appearance, metabolic transformation and plasma transport proteins of 14C-astaxanthin in Atlantic salmon (Salmo salar L.). Fish Physiol Biochem 21:325–334

  2. Alabaster J, Gough P (2006) The dissolved oxygen and temperature requirements of Atlantic salmon, Salmo salar L., in the Thames Estuary. J Fish Biol 29:613–621

  3. Amir A, McDonald D, Navas-Molina JA, Kopylova E, Morton J, Xu Z et al (2017) Deblur Rapidly resolves single-nucleotide community sequence patterns. mSystems 2:e00191–00116

  4. Anderson MJ (2001) A new method for non-parametric multivariate analysis of variance. Austral Ecol 26:32–46

  5. Apprill A (2017) Marine animal microbiomes: toward understanding host–microbiome interactions in a changing ocean. Front Mar Sci 4

  6. Austin B, Austin DA (1999) Bacterial fish pathogens. In: Bacterial fish pathogens: disease of farmed and wild fish. Springer Netherlands, 552 pp

  7. Baker RTM, Pfeiffer AM, Schöner FJ, Smith-Lemmon L (2002) Pigmenting efficacy of astaxanthin and canthaxanthin in fresh-water reared Atlantic salmon, Salmo salar. Anim Feed Sci Technol 99:97–106

  8. Bjerkeng B (2000) Carotenoid pigmentation of salmonid fishes recent progress. Avances en Nutricion Acuicola V. Memorias del V Simposium Internacional de Nutricion Acuicola 19–22 Noviembre, 2000. Merida, Yucatan. Retrieved from:

  9. Bokulich NA, Kaehler BD, Rideout JR, Dillon M, Bolyen E, Knight R et al (2018) Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin. Microbiome 6:90

  10. Bolnick DI, Snowberg LK, Hirsch PE, Lauber CL, Knight R, Caporaso JG, Svanback R (2014) Individuals’ diet diversity influences gut microbial diversity in two freshwater fish (threespine stickleback and Eurasian perch). Ecol Lett 17:979–987

  11. Borges P, Medale F, Veron V, Pires Mdos A, Dias J, Valente LM (2013) Lipid digestion, absorption and uptake in Solea senegalensis. Comp Biochem Physiol A Mol Integr Physiol 166:26–35

  12. Boronat A, Rodriguez-Concepcion M (2015) Terpenoid biosynthesis in prokaryotes. Adv Biochem Eng Biotechnol 148:3–18

  13. Braceland M, Bickerdike R, Tinsley J, Cockerill D, McLoughlin MF, Graham DA et al (2013) The serum proteome of Atlantic salmon, Salmo salar, during pancreas disease (PD) following infection with salmonid alphavirus subtype 3 (SAV3). J Proteome 94:423–436

  14. Cahoon L, Halkides C, Song B, Michael Williams C, Dubay GR, Fries A et al (2012) Swine waste as a source of natural products: a carotenoid antioxidant. 3

  15. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK et al (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7:335–336

  16. Caramujo M-J, de Carvalho CCCR, Silva SJ, Carman KR (2012) Dietary carotenoids regulate astaxanthin content of copepods and modulate their susceptibility to UV light and copper toxicity. Mar Drugs 10:998–1018

  17. Danulat E (1986) Role of bacteria with regard to chitin degradation in the digestive tract of the cod Gadus morhua. Mar Biol 90:335–343

  18. Davison JM, Lickwar CR, Song L, Breton G, Crawford GE, Rawls JF (2017) Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha. Genome Res 27:1195–1206

  19. de Matos GF, Zilli JE, de Araujo JLS, Parma MM, Melo IS, Radl V et al (2017) Bradyrhizobium sacchari sp. nov., a legume nodulating bacterium isolated from sugarcane roots. Arch Microbiol 199:1251–1258

  20. Dehler CE, Secombes CJ, Martin SAM (2017) Environmental and physiological factors shape the gut microbiota of Atlantic salmon parr (Salmo salar L.). Aquaculture 467:149–157

  21. Deming DM, Erdman John W (1999) Mammalian carotenoid absorption and metabolism. Pure Appl Chem 71:2213

  22. Duston J (1994) Effect of salinity on survival and growth of Atlantic salmon (Salmo salar) parr and smolts. Aquaculture 121:115–124

  23. Elliott JM, Elliott JA (2010) Temperature requirements of Atlantic salmon Salmo salar, brown trout Salmo trutta and Arctic charr Salvelinus alpinus: predicting the effects of climate change. J Fish Biol 77:1793–1817

  24. Gajardo K, Rodiles A, Kortner TM, Krogdahl Å, Bakke AM, Merrifield DL, Sørum H (2016) A high-resolution map of the gut microbiota in Atlantic salmon (Salmo salar): a basis for comparative gut microbial research. Sci Rep 6:30893

  25. Gao JL, Sun PB, Wang XM, Lv FY, Mao XJ, Sun JG (2017) Rhizobium wenxiniae sp. nov., an endophytic bacterium isolated from maize root. Int J Syst Evol Microbiol 67:2798–2803

  26. Garcia-Asua G, Lang HP, Cogdell RJ, Hunter CN (1998) Carotenoid diversity: a modular role for the phytoene desaturase step. Trends Plant Sci 3:445–449

  27. Garcia-Asua G, Cogdell RJ, Hunter CN (2002) Functional assembly of the foreign carotenoid lycopene into the photosynthetic apparatus of Rhodobacter sphaeroides, achieved by replacement of the native 3-step phytoene desaturase with its 4-step counterpart from Erwinia herbicola. Mol Microbiol 44:233–244

  28. Gatesoupe F-J, Infante J-LZ, Cahu C, Quazuguel P (1997) Early weaning of seabass larvae, Dicentrarchus labrax: the effect on microbiota, with particular attention to iron supply and exoenzymes. Aquaculture 158:117–127

  29. Gildberg A, Johansen A, Bøgwald J (1995) Growth and survival of Atlantic salmon (Salmo salar) fry given diets supplemented with fish protein hydrolysate and lactic acid bacteria during a challenge trial with Aeromonas salmonicida. Aquaculture 138:23–34

  30. Gómez GD, Balcázar JL (2008) A review on the interactions between gut microbiota and innate immunity of fish. FEMS Immunol Med Microbiol 52:145–154

  31. Grunenwald M, Adams MB, Carter CG, Nichols DS, Koppe W, Verlhac-Trichet V et al (2019) Pigment-depletion in Atlantic salmon (Salmo salar) post-smolt starved at elevated temperature is not influenced by dietary carotenoid type and increasing alpha-tocopherol level. Food Chem 299:125140

  32. Hannibal L, Lorquin J, D’Ortoli NA, Garcia N, Chaintreuil C, Masson-Boivin C et al (2000) Isolation and characterization of canthaxanthin biosynthesis genes from the photosynthetic bacterium Bradyrhizobium sp. strain ORS278. J Bacteriol 182:3850–3853

  33. Henrikson C V (1966) Growth Response of Mycoplasma to Carotenoid Pigments and Carotenoid Intermediates. J Gen Microbiol 45:73–52.

  34. Heuston S, Begley M, Gahan CG, Hill C (2012) Isoprenoid biosynthesis in bacterial pathogens. Microbiology 158:1389–1401

  35. Hill GE (1999) Is there an immunological cost to carotenoid-based ornamental coloration? Am Nat 154:589–595

  36. Ichiyama S, Shimokata K, Tsukamura M (1988) Relationship between mycobacterial species and their carotenoid pigments. Microbiol Immunol 32:473–479

  37. Ivanov II, Littman DR (2010) Segmented filamentous bacteria take the stage. Mucosal Immunol 3:209–212

  38. Komori M, Ghosh R, Takaichi S, Hu Y, Mizoguchi T, Koyama Y, Kuki M (1998) A null lesion in the rhodopin 3,4-desaturase of rhodospirillum rubrum unmasks a cryptic branch of the carotenoid biosynthetic pathway. Biochemistry 37:8987–8994

  39. Langille MGI, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA et al (2013) Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol 31:814

  40. Lindsay GJH, Harris JE (1980) Carboxymethylcellulase activity in the digestive tracts of fish. J Fish Biol 16:219–233

  41. Liu Y, de Bruijn I, Jack ALH, Drynan K, van den Berg AH, Thoen E et al (2014) Deciphering microbial landscapes of fish eggs to mitigate emerging diseases. ISME J 8:2002–2014

  42. Llewellyn MS, Leadbeater S, Garcia C, Sylvain FE, Custodio M, Ang KP et al (2017) Parasitism perturbs the mucosal microbiome of Atlantic Salmon. Sci Rep 7:43465

  43. Lokesh J, Kiron V, Sipkema D, Fernandes JMO, Moum T (2019) Succession of embryonic and the intestinal bacterial communities of Atlantic salmon (Salmo salar) reveals stage-specific microbial signatures. MicrobiologyOpen 8:e00672

  44. Lozano GA (1994) Carotenoids, parasites, and sexual selection. Oikos 70:309–311

  45. Lozupone C, Knight R (2005) UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 71:8228–8235

  46. Ludwig JA, Reynolds JF (1988) Statistical ecology: a primer on methods & computing. Wiley, New York

  47. Maquelin K, Hoogenboezem T, Jachtenberg J-W, Dumke R, Jacobs E, Puppels GJ et al (2009) Raman spectroscopic typing reveals the presence of carotenoids in Mycoplasma pneumoniae. Microbiology 155:2068–2077

  48. Matthews SJ, Ross NW, Lall SP, Gill TA (2006) Astaxanthin binding protein in Atlantic salmon. Comp Biochem Physiol B Biochem Mol Biol 144:206–214

  49. McGarvey DJ, Croteau R (1995) Terpenoid metabolism. Plant Cell 7:1015–1026

  50. Melancon E, De La Torre Canny SG, Sichel S, Kelly M, Wiles TJ, Rawls JF et al (2017) Best practices for germ-free derivation and gnotobiotic zebrafish husbandry. Methods Cell Biol 138:61–100

  51. Merrifield DL, Dimitroglou A, Bradley G, Baker RTM, Davies SJ (2009) Soybean meal alters autochthonous microbial populations, microvilli morphology and compromises intestinal enterocyte integrity of rainbow trout, Oncorhynchus mykiss (Walbaum). J Fish Dis 32:755–766

  52. Merrifield DL, Dimitroglou A, Foey A, Davies SJ, Baker RTM, Bøgwald J et al (2010) The current status and future focus of probiotic and prebiotic applications for salmonids. Aquaculture 302:1–18

  53. Morton JT, Sanders J, Quinn RA, McDonald D, Gonzalez A, Vázquez-Baeza Y et al (2017) Balance trees reveal microbial niche differentiation. mSystems 2

  54. Navarrete P, Espejo RT, Romero J (2009) Molecular analysis of microbiota along the digestive tract of juvenile Atlantic salmon (Salmo salar L.). Microb Ecol 57:550–561

  55. Negi S, Singh H, Mukhopadhyay A (2017) Gut bacterial peptides with autoimmunity potential as environmental trigger for late onset complex diseases: in–silico study. PLoS One 12:e0180518

  56. Neuman C, Hatje E, Bowman J, Stevenson H, Katouli M (2012). The effect of diet and environmental temperature on gut microflora of Atlantic Salmon

  57. Neuman C, Hatje E, Zarkasi KZ, Smullen R, Bowman JP, Katouli M (2016) The effect of diet and environmental temperature on the faecal microbiota of farmed Tasmanian Atlantic Salmon (Salmo salar L.). 47:660–672

  58. Price MN, Dehal PS, Arkin AP (2010) FastTree 2 – approximately maximum-likelihood trees for large alignments. PLoS One 5:e9490

  59. Rajasingh H, Øyehaug L, Våge DI, Omholt SW (2006) Carotenoid dynamics in Atlantic salmon. BMC Biol 4:10

  60. Rawls JF, Samuel BS, Gordon JI (2004) Gnotobiotic zebrafish reveal evolutionarily conserved responses to the gut microbiota. Proc Natl Acad Sci U S A 101:4596–4601

  61. Ray AK, Ghosh K, Ringo E (2012) Enzyme-producing bacteria isolated from fish gut: a review. Aquac Nutr 18:465–492

  62. Remen M, Sievers M, Torgersen T, Oppedal F (2016) The oxygen threshold for maximal feed intake of Atlantic salmon post-smolts is highly temperature-dependent. Aquaculture 464

  63. Reveco FE, Øverland M, Romarheim OH, Mydland LT (2014) Intestinal bacterial community structure differs between healthy and inflamed intestines in Atlantic salmon (Salmo salar L.). Aquaculture 420–421:262–269

  64. Ringø E, Salinas I, Olsen RE, Nyhaug A, Myklebust R, Mayhew TM (2007) Histological changes in intestine of Atlantic salmon (Salmo salar L.) following in vitro exposure to pathogenic and probiotic bacterial strains. Cell Tissue Res 328:109–116

  65. Roeselers G, Mittge EK, Stephens WZ, Parichy DM, Cavanaugh CM, Guillemin K, Rawls JF (2011) Evidence for a core gut microbiota in the zebrafish. Isme J 5:1595–1608

  66. Rognes T, Flouri T, Nichols B, Quince C, Mahé F (2016) VSEARCH: a versatile open source tool for metagenomics. PeerJ 4:e2584

  67. Rud I, Kolarevic J, Holan AB, Berget I, Calabrese S, Terjesen BF (2017) Deep-sequencing of the bacterial microbiota in commercial-scale recirculating and semi-closed aquaculture systems for Atlantic salmon post-smolt production. Aquac Eng 78:50–62

  68. Rye M, Gjerde B (1996) Phenotypic and genetic parameters of body composition traits and flesh color in Atlantic salmon, Salmo salar L. Aquac Res 27:121–133

  69. Saini RK, Keum Y-S (2017) Progress in microbial carotenoids production. Indian J Microbiol 57:129–130

  70. Schmidt VT, Smith KF, Melvin DW, Amaral-Zettler LA (2015) Community assembly of a euryhaline fish microbiome during salinity acclimation. Mol Ecol 24:2537–2550

  71. Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, Huttenhower C (2011) Metagenomic biomarker discovery and explanation. Genome Biol 12:R60

  72. Sheng Y, Ren H, Limbu SM, Sun Y, Qiao F, Zhai W et al (2018) The presence or absence of intestinal microbiota affects lipid deposition and related genes expression in zebrafish (Danio rerio). Front Microbiol 9

  73. Sigurgisladottir S, ØTorrissen O, Lie Ø, Thomassen M, Hafsteinsson H (1997) Salmon quality: methods to determine the quality parameters. Rev Fish Sci 5:223–252

  74. Small CM, Milligan-Myhre K, Bassham S, Guillemin K, Cresko WA (2017) Host genotype and microbiota contribute asymmetrically to transcriptional variation in the threespine stickleback gut. Genome Biol Evol 9:504–520

  75. Smith PF (1963) The carotenoid pigments of mycoplasma. J Gen Microbiol 32:307–319

  76. Smith CVHAPF (1966) Growth response of mycoplasma to carotenoid pigments and carotenoid intermediates. J Gen Microbiol 45:73–52

  77. Smith PF, Rothblat GH (1962) Comparison of lipid composition of pleuropneumonia-like and L-type organisms. J Bacteriol 83:500–506

  78. Star B, Haverkamp TH, Jentoft S, Jakobsen KS (2013) Next generation sequencing shows high variation of the intestinal microbial species composition in Atlantic cod caught at a single location. BMC Microbiol 13:248

  79. Stehfest KM, Carter CG, McAllister JD, Ross JD, Semmens JM (2017) Response of Atlantic salmon Salmo salar to temperature and dissolved oxygen extremes established using animal-borne environmental sensors. Sci Rep 7:4545–4545

  80. Sugita H, Kawasaki J, Deguchi Y (1997) Production of amylase by the intestinal microflora in cultured freshwater fish. Lett Appl Microbiol 24:105–108

  81. Torrissen OJ (1995) Strategies for salmonid pigmentation. J Appl Ichthyol 11:276–281

  82. Torrissen O, Hardy RW, Shearer K (1989) Pigmentation of salmonids: carotenoid deposition and metabolism. 1

  83. Umeno D, Tobias AV, Arnold FH (2005) Diversifying carotenoid biosynthetic pathways by directed evolution. Microbiol Mol Biol Rev 69:51–78

  84. Uren Webster TM, Consuegra S, Hitchings M, Garcia de Leaniz C (2018) Interpopulation variation in the atlantic salmon microbiome reflects environmental and genetic diversity. Appl Environ Microbiol 84

  85. Vázquez-Baeza Y, Pirrung M, Gonzalez A, Knight R (2013) EMPeror: a tool for visualizing high-throughput microbial community data. GigaScience 2:16

  86. Vázquez-Baeza Y, Gonzalez A, Smarr L, McDonald D, Morton JT, Navas-Molina JA, Knight R (2017) Bringing the dynamic microbiome to life with animations. Cell Host Microbe 21:7–10

  87. Vikeså V, Nankervis L, Hevrøy E (2016) Appetite, metabolism and growth regulation in Atlantic salmon (Salmo salar L.) exposed to hypoxia at elevated seawater temperature. Aquac Res.

  88. Wade N, Goulter KC, Wilson KJ, Hall MR, Degnan BM (2005) Esterified astaxanthin levels in lobster epithelia correlate with shell color intensity: potential role in crustacean shell colour formation. Comp Biochem Physiol B Biochem Mol Biol 141:307–313

  89. Wade NM, Clark TD, Maynard BT, Atherton S, Wilkinson RJ, Smullen RP, Taylor RS (2019) Effects of an unprecedented summer heatwave on the growth performance, flesh colour and plasma biochemistry of marine cage-farmed Atlantic salmon (Salmo salar). J Therm Biol 80:64–74

  90. White DA, Page GI, Swaile J, Moody AJ, Davies SJ (2002) Effect of esterification on the absorption of astaxanthin in rainbow trout, Oncorhynchus mykiss (Walbaum). Aquac Res 33:343–350

  91. Xia JH, Lin G, Fu GH, Wan ZY, Lee M, Wang L et al (2014) The intestinal microbiome of fish under starvation. BMC Genomics 15:266

  92. Xuedong Zhou YL (2015) Chapter 5 - oral mucosal microbes. In: Zhou X, Li Y (eds) Atlas of oral microbiology. Academic Press, Oxford, pp 95–107

  93. Zakrzewski M, Proietti C, Ellis JJ, Hasan S, Brion M-J, Berger B, Krause L (2017) Calypso: a user-friendly web-server for mining and visualizing microbiome–environment interactions. Bioinformatics 33:782–783

  94. Zaripheh S, Erdman JW Jr (2002) Factors that influence the bioavailablity of xanthophylls. J Nutr 132:531s–534s

  95. Zarkasi KZ, Abell GCJ, Taylor RS, Neuman C, Hatje E, Tamplin ML et al (2014) Pyrosequencing-based characterization of gastrointestinal bacteria of Atlantic salmon (Salmo salar L.) within a commercial mariculture system. J Appl Microbiol 117:18–27

  96. Zarkasi KZ, Taylor RS, Abell GCJ, Tamplin ML, Glencross BD, Bowman JP (2016) Atlantic salmon (Salmo salar L.) gastrointestinal microbial community dynamics in relation to digesta properties and diet. Microb Ecol 71:589–603

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The authors would like to acknowledge Petuna Aquaculture, Stuart Atherton, Tom Fox-Smith, and Ryan Wilkinson for their contribution to this project.


The research was funded by the Fisheries Research and Development Corporation FRDC (project code: FRDC 2014-248) through a collaboration between Petuna Aquaculture and the University of the Sunshine Coast. CDHN was supported by an International postgraduate award from the University of the Sunshine Coast.

Author information

Conceived and designed the experiments: CDHN, GA, TV, and AE. Collected samples: GA. Performed the experiments: CDHN. Analyzed the data: CDHN and JM. Wrote the paper: CDHN. All authors contributed to the paper drafts and accepted the manuscript.

Correspondence to Abigail Elizur.

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All procedures were carried out with the approval of the University of the Sunshine Coast Animal Ethics Committee (AN/E/16/12).

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Nguyen, C.D.H., Amoroso, G., Ventura, T. et al. Atlantic Salmon (Salmo salar L., 1758) Gut Microbiota Profile Correlates with Flesh Pigmentation: Cause or Effect?. Mar Biotechnol (2020).

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  • Atlantic salmon
  • Microbiota
  • Flesh color
  • Pigmentation
  • Carotenoids