Abstract
Although understood in many vertebrate systems, the natural diversity of host-associated microbiota has been little studied in teleosts. For migratory fishes, successful exploitation of multiple habitats may affect and be affected by the composition of the intestinal microbiome. We collected 96 Salmo salar from across the Atlantic encompassing both freshwater and marine phases. Dramatic differences between environmental and gut bacterial communities were observed. Furthermore, community composition was not significantly impacted by geography. Instead life-cycle stage strongly defined both the diversity and identity of microbial assemblages in the gut, with evidence for community destabilisation in migratory phases. Mycoplasmataceae phylotypes were abundantly recovered in all life-cycle stages. Patterns of Mycoplasmataceae phylotype recruitment to the intestinal microbial community among sites and life-cycle stages support a dual role for deterministic and stochastic processes in defining the composition of the S. salar gut microbiome.
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Acknowledgements
We thank the assistance of Julien April and Denise Deschamps, Ministère des Ressources Naturelles et de la Faune, Quebec Canada; Tim Sheehan, NOAA Fisheries Service; Woods Hole, USA; Ger Rogan, Russell Poole, Katie Thomas, Niall O’Maoileidigh, Deirdre Cotter and Elvira de Eyto, Marine Institute, Ireland; Paddy Gargan and Michael Hughes, Inland Fisheries Ireland; and Brian Clarke and Tom Reed, University College Cork in sample collection. MSL was funded by a Marie Skłodowska-Curie International Outgoing Fellowship, grant number 302503. JL was funded by a NSERC-CREATE Fellowship. FT was funded by a NSERC discovery grant awarded to ND. PMcG was supported by the Beaufort Marine Fish Award in Fish Population Genetics funded by the Irish Government under the Sea Change Programme.
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Llewellyn, M., McGinnity, P., Dionne, M. et al. The biogeography of the atlantic salmon (Salmo salar) gut microbiome. ISME J 10, 1280–1284 (2016). https://doi.org/10.1038/ismej.2015.189
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DOI: https://doi.org/10.1038/ismej.2015.189
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