Characterization of mid-intestinal microbiota of farmed Chinook salmon using 16S rRNA gene metabarcoding

Authors

  • Milica Ciric Ministry for Primary Industries, Investigation and Diagnostic Centre, Animal Health Laboratory, 66 Ward Street, Wallaceville, Upper Hutt, New Zealand Present address: Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11010 Belgrade http://orcid.org/0000-0002-5709-7136
  • David Waite Ministry for Primary Industries, Investigation and Diagnostic Centre, Plant Health and Environment Laboratory, PO Box 2095, Auckland, New Zealand Present address: Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072 http://orcid.org/0000-0002-0184-2942
  • Jenny Draper Ministry for Primary Industries, Investigation and Diagnostic Centre, Animal Health Laboratory, 66 Ward Street, Wallaceville, Upper Hutt, New Zealand Present address: Institute of Environmental Science and Research Limited (ESR), Kenepuru Science Centre, 34 Kenepuru Drive, Kenepuru, Porirua 5022, PO Box 50348, Porirua 5240 http://orcid.org/0000-0002-6916-6442
  • John Brian Jones Ministry for Primary Industries, Investigation and Diagnostic Centre, Animal Health Laboratory, 66 Ward Street, Wallaceville, Upper Hutt, New Zealand Present address: Murdoch University, 90 South St, Murdoch, WA 6150 http://orcid.org/0000-0002-0773-2007

Keywords:

farmed salmon, mid-intestinal microbiota, partial 16S rRNA gene sequencing

Abstract

Paper description:

  • With worldwide growth of aquaculture, the characterization of microbiota of high-value aquaculture species is of special interest.
  • This paper reports a novel workflow for high-throughput surveys of bacterial intestinal microbiota of aquacultured fish using metabarcode profiling of the V3-V4 hypervariable region of the bacterial 16S rRNA gene.
  • The workflow was used to produce the first 16S rRNA gene metabarcoding survey of the mid-intestinal microbiota of farmed Chinook salmon.
  • The presented workflow could be applied to other aquacultured fish species to capture variation or dysbiosis occurring as a result of changes in feed, health or environmental conditions.


Abstract: With the growing importance of aquaculture worldwide, characterization of the microbiota of high-value aquaculture species and identification of their shifts induced by changes in fish physiology or nutrition is of special interest. Here we report the first 16S rRNA gene metabarcoding survey of the mid-intestinal bacteria of Chinook salmon (Oncorhynchus tshawytscha), an economically important aquacultured species. The microbiota of 30 farmed Chinook salmon from a single cohort was surveyed using metabarcode profiling of the V3-V4 hypervariable region of the bacterial 16S rRNA gene. Seawater, feed and mid-intestinal samples and controls were sequenced in quadruplicate to assess both biological and technical variation in the microbial profiles. Over 1000 operational taxonomic units were identified within the cohort, providing a first glimpse into the mid-intestinal microbiota of farmed Chinook salmon. The taxonomic distribution of the salmon microbiota was reasonably stable, with around two thirds of individuals dominated by members of the family Vibrionaceae. We anticipate that the workflow presented in this paper could be applied in other aquacultured fish species to capture variation or dysbiosis occurring as a result of changes in feed, health or environmental conditions.

https://doi.org/10.2298/ABS190402040C

Received: April 2, 2019; Revised: June 15, 2019; Accepted: July 3, 2019; Published online: July 17, 2019

How to cite this article: 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):577-87.

Downloads

Download data is not yet available.

References

Llewellyn MS, Boutin S, Hoseinifar SH, Derome N. Teleost microbiomes: the state of the art in their characterization, manipulation and importance in aquaculture and fisheries. Front Microbiol. 2014;5: 207.

Nelson JS, Grande TC, Mark WVH. Fishes of the World, 5th Edition. New York: John Wiley & Sons; 2016.

Nayak SK. Role of gastrointestinal microbiota in fish. Aquac Res. 2010;41(11):1553–73.

Tarnecki AM, Burgos FA, Ray CL, Arias CR. Fish Intestinal Microbiome: Diversity and Symbiosis Unraveled by Metagenomics. J Appl Microbiol. 2017;123(1):2-17.

Ghanbari M, Kneifel W, Domig KJ. A new view of the fish gut microbiome: Advances from next-generation sequencing. Aquaculture. 2015;448:464–75.

Navarrete P, Espejo RT, Romero J. Molecular analysis of microbiota along the digestive tract of juvenile Atlantic salmon (Salmo salar L.). Microb Ecol. 2009;57(3):550–61.

Romero J, Ringø E, Merrifield DL. The Gut Microbiota of Fish. In: Aquaculture Nutrition. Chichester, UK: John Wiley & Sons, Ltd; 2014. p. 75–100.

Gómez GD, Balcázar JL. A review on the interactions between gut microbiota and innate immunity of fish. FEMS Immunol Med Microbiol. 2008;52(2):145–54.

Mouchet MA, Bouvier C, Bouvier T, Troussellier M, Escalas A, Mouillot D. Genetic difference but functional similarity among fish gut bacterial communities through molecular and biochemical fingerprints. FEMS Microbiol Ecol. 2012;79(3):568–80.

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

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.

Larsen AM, Mohammed HH, Arias CR. Comparison of DNA extraction protocols for the analysis of gut microbiota in fishes. FEMS Microbiol Lett. 2015;362(5).

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.

Egerton S, Culloty S, Whooley J, Stanton C, Ross RP. The gut microbiota of marine fish. Front Microbiol. 2018;9.

Givens C, Ransom B, Bano N, Hollibaugh J. Comparison of the gut microbiomes of 12 bony fish and 3 shark species. Mar Ecol Prog Ser. 2015;518:209–23.

Sullam KE, Essinger SD, Lozupone CA, O’Connor MP, Rosen GL, Knight R, Kilham SS, Russell JA. Environmental and ecological factors that shape the gut bacterial communities of fish: a meta-analysis. Mol Ecol. 2012;21(13):3363–78.

Izvekova GI, Izvekov EI, Plotnikov AO. Symbiotic microflora in fishes of different ecological groups. Izv Akad Nauk Seriia Biol. 2007;(6):728–37.

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.

Holben WE, Williams P, Gilbert MA, 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.

Hovda MB, Fontanillas R, McGurk C, Obach A, Rosnes JT. Seasonal variations in the intestinal microbiota of farmed Atlantic salmon (Salmo salar L.). Aquac Res. 2012;43(1):154–9.

Hovda MB, Lunestad BT, Fontanillas R, Rosnes JT. Molecular characterisation of the intestinal microbiota of farmed Atlantic salmon (Salmo salar L.). Aquaculture. 2007;272(1):581–8.

Skrodenyte-Arbaciauskiene V, Sruoga A, Butkauskas D, Skrupskelis K. Phylogenetic analysis of intestinal bacteria of freshwater salmon Salmo salar and sea trout Salmo trutta trutta and diet. Fish Sci. 2008;74(6):1307–14.

Zarkasi KZ, Abell GCJ, Taylor RS, Neuman C, Hatje E, Tamplin ML, Katouli M, Bowman JP. 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.

Romero J, Navarrete P. 16S rDNA-based analysis of dominant bacterial populations associated with early life stages of coho salmon (Oncorhynchus kisutch). Microb Ecol. 2006;51(4):422–30.

Desai AR, Links MG, Collins SA, Mansfield GS, Drew MD, Van Kessel AG, Hill JE. Effects of plant-based diets on the distal gut microbiome of rainbow trout (Oncorhynchus mykiss). Aquaculture. 2012;350:134–42.

Jaafar RM, Kania PW, Larsen AH, Nielsen DS, Fouz B, Browdy C, Buchmann K. Gut microbiota changes in rainbow trout, Oncorhynchus mykiss (Walbaum), during organic acid feed supplementation and Yersinia ruckeri infection. J Fish Dis. 2013;36(6):599–606.

Mansfield GS, Desai AR, Nilson SA, Van Kessel AG, Drew MD, Hill JE. Characterization of rainbow trout (Oncorhynchus mykiss) intestinal microbiota and inflammatory marker gene expression in a recirculating aquaculture system. Aquaculture. 2010;307(1):95–104.

Navarrete P, Magne F, Araneda C, Fuentes P, Barros L, Opazo R, Espejo R, Romero J. PCR-TTGE analysis of 16S rRNA from rainbow trout (Oncorhynchus mykiss) gut microbiota reveals host-specific communities of active bacteria. PLoS One. 2012;7(2):e31335.

Navarrete P, Magne F, Mardones P, Riveros M, Opazo R, Suau A, Pochart P, Romero J. Molecular analysis of intestinal microbiota of rainbow trout (Oncorhynchus mykiss). FEMS Microbiol Ecol. 2010;71(1):148–56.

New Zealand King Salmon Report. 2011 [cited 2016 Nov 6]. Available from: https://www.epa.govt.nz/assets/FileAPI/proposal/NSP000002/Applicants-proposal-documents/6e18a60c5b/Appendix-2-NZ-King-Salmon-Report.pdf.

Camara MD, Symonds JE. Genetic improvement of New Zealand aquaculture species: Programmes, progress and prospects. NZJ Mar Freshwater Res. 2014;48(3):466–91.

Salter SJ, Cox MJ, Turek EM, Calus ST, Cookson WO, Moffatt MF, Turner P, Parkhill J, Loman NJ, Walker AW. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol. 2014;12(87).

BEI Resources. HM-782D Mixed bacteria, Genomic DNA from Microbial Mock Community B (Even, Low Concentration), v5.1L, for 16S rRNA Gene Sequencing. 2014 [cited 2016 Nov 6]. Available from: https://www.beiresources.org/Catalog/otherProducts/HM-782D.aspx .

Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, Huttley GA. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7(5):335-6.

Jervis-Bardy J, Leong LEX, Marri S, Smith RJ, Choo JM, Smith-Vaughan HC, Nosworthy E, Morris PS, O’Leary S, Rogers GB, Marsh RL. Deriving accurate microbiota profiles from human samples with low bacterial content through post-sequencing processing of Illumina MiSeq data. Microbiome. 2015;3(19).

Sauter S, McMillan J, Dunham J. Salmonid Behavior and Water Temperature. 2001 [cited 2016 Sep 17]. Available from: https://nepis.epa.gov/Exe/ZyPDF.cgi/P100TNSE.PDF?Dockey=P100TNSE.PDF.

Smriga S, Sandin SA, Azam F. Abundance, diversity, and activity of microbial assemblages associated with coral reef fish guts and feces. FEMS Microbiol Ecol. 2010;73(1):31–42.

Martin-Antonio B, Manchado M, Infante C, Zerolo R, Labella A, Alonso C, Borrego JJ. Intestinal microbiota variation in Senegalese sole (Solea senegalensis) under different feeding regimes. Aquac Res. 2007;38(11):1213–22.

Roeselers G, Mittge EK, Stephens WZ, Parichy DM, Cavanaugh CM, Guillemin K, Rawls JF. Evidence for a core gut microbiota in the zebrafish. ISME J. 2011;5(10):1595–608.

Ward NL, Steven B, Penn K, Methé BA, Detrich WH. Characterization of the intestinal microbiota of two Antarctic notothenioid fish species. Extremophiles. 2009;13(4):679–85.

Shafquat A, Joice R, Simmons SL, Huttenhower C. Functional and phylogenetic assembly of microbial communities in the human microbiome. Trends Microbiol. 2014;22(5):261–6.

Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, Sogin ML, Jones WJ, Roe BA, Affourtit JP, Egholm M, Henrissat B, Heath AC, Knight R, Gordon JI. A core gut microbiome in obese and lean twins. Nature. 2009;457(7228):480–4.

Xia JH, Lin G, Fu GH, Wan ZY, Lee M, Wang L, Liu XJ, Yue GH. The intestinal microbiome of fish under starvation. BMC Genomics. 2014;15(266).

Vasanth G, Kiron V, Kulkarni A, Dahle D, Lokesh J, Kitani Y. A Microbial Feed Additive Abates Intestinal Inflammation in Atlantic Salmon. Front Immunol. 2015;6:409.

Brosnahan CL, Ha HJ, Booth K, McFadden AMJ, Jones JB. First report of a rickettsia-like organism from farmed Chinook salmon, Oncorhynchus tshawytscha (Walbaum), in New Zealand. New Zeal J Mar Freshw Res. 2017;51(3):356–69.

Gias E, Draper J, Brosnahan CL, Orr D, McFadden A, Jones B. Draft Genome Sequence of a New Zealand Rickettsia-Like Organism Isolated from Farmed Chinook Salmon. Genome Announc. 2016;4(3):e00503-16.

Wang Y, Qian P-Y, Methe B, Lovley D, Chandler D. Conservative Fragments in Bacterial 16S rRNA Genes and Primer Design for 16S Ribosomal DNA Amplicons in Metagenomic Studies. PLoS One. 2009;4(10):e7401.

Yarza P, Yilmaz P, Pruesse E, Glöckner FO, Ludwig W, Schleifer K-H, Whitman WB, Euzéby J, Amann R, Rosselló-Móra R. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol. 2014;12(9):635–45.

Rozas M, Enríquez R. Piscirickettsiosis and Piscirickettsia salmonis in fish: a review. J Fish Dis. 2014;37(3):163–88.

Goodrich JK, Di Rienzi SC, Poole AC, Koren O, Walters WA, Caporaso JG, Knight R, Ley RE. Conducting a microbiome study. Cell. 2014;158(2):250–62.

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.

Yan Q, Li J, Yu Y, Wang J, He Z, Van Nostrand JD, Kempher ML, Wu L, Wang Y, Liao L, Li X, Wu S, Ni J, Wang C, Zhou J. Environmental filtering decreases with fish development for the assembly of gut microbiota. Environ Microbiol. 2016;18(12):4739–54.

Downloads

Published

2019-12-19

How to Cite

1.
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 [Internet]. 2019Dec.19 [cited 2022Aug.18];71(4):577-8. Available from: https://www.serbiosoc.org.rs/arch/index.php/abs/article/view/4144

Issue

Section

Articles