title: The biogeography of the atlantic salmon (Salmo salar) gut microbiome.
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.
authors.affiliation: Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Environment Centre Wales, Bangor, UK.|Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec City, Quebec, Canada.|Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK.
authors.forename: Martin S
authors.initials: MS
authors.lastname: Llewellyn
authors.affiliation: School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland.
authors.forename: Philip
authors.initials: P
authors.lastname: McGinnity
authors.affiliation: Ministère des Ressources Naturelles et de la Faune, Quebec City, Quebec, Canada.
authors.forename: Melanie
authors.initials: M
authors.lastname: Dionne
authors.affiliation: Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec City, Quebec, Canada.
authors.forename: Justine
authors.initials: J
authors.lastname: Letourneau
authors.affiliation: Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec City, Quebec, Canada.
authors.forename: Florian
authors.initials: F
authors.lastname: Thonier
authors.affiliation: Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Environment Centre Wales, Bangor, UK.
authors.forename: Gary R
authors.initials: GR
authors.lastname: Carvalho
authors.affiliation: Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Environment Centre Wales, Bangor, UK.
authors.forename: Simon
authors.initials: S
authors.lastname: Creer
authors.affiliation: Institut de Biologie Intégrative et des Systèmes, Université Laval, Quebec City, Quebec, Canada.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Derome
mesh_terms: D000818:Animals; D044822:Biodiversity; D019295:Computational Biology; D004777:Environment; D005618:Fresh Water; D000069196:Gastrointestinal Microbiome; D005843:Geography; D007422:Intestines / Q000382:microbiology*; D008018:Life Cycle Stages; D064307:Microbiota; D020317:Salmo salar / Q000382:microbiology*