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Interpopulation Variation in the Atlantic Salmon Microbiome Reflects Environmental and Genetic Diversity

Tamsyn Uren Webster Orcid Logo, Sofia Consuegra, Matthew Hitchings Orcid Logo, Carlos Garcia De Leaniz Orcid Logo, Sofia Consuegra del Olmo Orcid Logo

Applied and Environmental Microbiology, Volume: 84, Issue: 16

Swansea University Authors: Tamsyn Uren Webster Orcid Logo, Matthew Hitchings Orcid Logo, Carlos Garcia De Leaniz Orcid Logo, Sofia Consuegra del Olmo Orcid Logo

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DOI (Published version): 10.1128/AEM.00691-18

Abstract

The microbiome has a crucial influence on host phenotype, and is of broad interest to ecological and evolutionary research. Yet, the extent of variation that occurs in the microbiome within and between populations is unclear. We characterised the skin and gut microbiome of seven populations of juven...

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Published in: Applied and Environmental Microbiology
ISSN: 0099-2240 1098-5336
Published: American Society for Microbiology 2018
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URI: https://cronfa.swan.ac.uk/Record/cronfa40815
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Yet, the extent of variation that occurs in the microbiome within and between populations is unclear. We characterised the skin and gut microbiome of seven populations of juvenile Atlantic salmon (Salmo salar) inhabiting a diverse range of environments, including hatchery-reared and wild populations. We found shared skin OTUs across all populations and core gut microbiota for all wild fish, but the diversity and structure of both skin and gut microbial communities were distinct between populations. There was a marked difference between the gut microbiome of wild and captive fish. Hatchery-reared fish had lower intestinal microbial diversity, lacked core microbiota found in wild fish, and showed altered community structure and function. Captive fish skin and gut microbiomes were also less variable within populations, reflecting more uniform artificial rearing conditions. Surrounding water influenced the microbiome of the gut and, especially, the skin, but could not explain the degree of variation observed between populations. For both the gut and skin, we found that there was greater difference in microbial community structure between more genetically distinct fish populations, and also that population genetic diversity was positively correlated with microbiome diversity. However, diet is likely to be the major factor contributing to the large differences in gut microbiota between wild and captive fish. 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spelling 2022-12-05T16:05:23.4160581 v2 40815 2018-06-26 Interpopulation Variation in the Atlantic Salmon Microbiome Reflects Environmental and Genetic Diversity 3ea91c154926c86f89ea6a761122ecf6 0000-0002-0072-9745 Tamsyn Uren Webster Tamsyn Uren Webster true false be98847c72c14a731c4a6b7bc02b3bcf 0000-0002-5527-4709 Matthew Hitchings Matthew Hitchings true false 1c70acd0fd64edb0856b7cf34393ab02 0000-0003-1650-2729 Carlos Garcia De Leaniz Carlos Garcia De Leaniz true false 241f2810ab8f56be53ca8af23e384c6e 0000-0003-4403-2509 Sofia Consuegra del Olmo Sofia Consuegra del Olmo true false 2018-06-26 SBI The microbiome has a crucial influence on host phenotype, and is of broad interest to ecological and evolutionary research. Yet, the extent of variation that occurs in the microbiome within and between populations is unclear. We characterised the skin and gut microbiome of seven populations of juvenile Atlantic salmon (Salmo salar) inhabiting a diverse range of environments, including hatchery-reared and wild populations. We found shared skin OTUs across all populations and core gut microbiota for all wild fish, but the diversity and structure of both skin and gut microbial communities were distinct between populations. There was a marked difference between the gut microbiome of wild and captive fish. Hatchery-reared fish had lower intestinal microbial diversity, lacked core microbiota found in wild fish, and showed altered community structure and function. Captive fish skin and gut microbiomes were also less variable within populations, reflecting more uniform artificial rearing conditions. Surrounding water influenced the microbiome of the gut and, especially, the skin, but could not explain the degree of variation observed between populations. For both the gut and skin, we found that there was greater difference in microbial community structure between more genetically distinct fish populations, and also that population genetic diversity was positively correlated with microbiome diversity. However, diet is likely to be the major factor contributing to the large differences in gut microbiota between wild and captive fish. Our results highlight the scope of inter-population variation in the Atlantic salmon microbiome, and offer insights into the deterministic factors contributing to this. Journal Article Applied and Environmental Microbiology 84 16 American Society for Microbiology 0099-2240 1098-5336 31 8 2018 2018-08-31 10.1128/AEM.00691-18 COLLEGE NANME Biosciences COLLEGE CODE SBI Swansea University RCUK, BB/M026469/1 2022-12-05T16:05:23.4160581 2018-06-26T15:31:54.3969892 Faculty of Science and Engineering School of Biosciences, Geography and Physics - Biosciences Tamsyn Uren Webster 0000-0002-0072-9745 1 Sofia Consuegra 2 Matthew Hitchings 0000-0002-5527-4709 3 Carlos Garcia De Leaniz 0000-0003-1650-2729 4 Sofia Consuegra del Olmo 0000-0003-4403-2509 5 0040815-15082018110012.pdf 40815VoR.pdf 2018-08-15T11:00:12.0330000 Output 3049332 application/pdf Version of Record true 2018-08-15T00:00:00.0000000 Distributed under the terms of a Creative Commons CC-BY Licence. true eng
title Interpopulation Variation in the Atlantic Salmon Microbiome Reflects Environmental and Genetic Diversity
spellingShingle Interpopulation Variation in the Atlantic Salmon Microbiome Reflects Environmental and Genetic Diversity
Tamsyn Uren Webster
Matthew Hitchings
Carlos Garcia De Leaniz
Sofia Consuegra del Olmo
title_short Interpopulation Variation in the Atlantic Salmon Microbiome Reflects Environmental and Genetic Diversity
title_full Interpopulation Variation in the Atlantic Salmon Microbiome Reflects Environmental and Genetic Diversity
title_fullStr Interpopulation Variation in the Atlantic Salmon Microbiome Reflects Environmental and Genetic Diversity
title_full_unstemmed Interpopulation Variation in the Atlantic Salmon Microbiome Reflects Environmental and Genetic Diversity
title_sort Interpopulation Variation in the Atlantic Salmon Microbiome Reflects Environmental and Genetic Diversity
author_id_str_mv 3ea91c154926c86f89ea6a761122ecf6
be98847c72c14a731c4a6b7bc02b3bcf
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241f2810ab8f56be53ca8af23e384c6e
author_id_fullname_str_mv 3ea91c154926c86f89ea6a761122ecf6_***_Tamsyn Uren Webster
be98847c72c14a731c4a6b7bc02b3bcf_***_Matthew Hitchings
1c70acd0fd64edb0856b7cf34393ab02_***_Carlos Garcia De Leaniz
241f2810ab8f56be53ca8af23e384c6e_***_Sofia Consuegra del Olmo
author Tamsyn Uren Webster
Matthew Hitchings
Carlos Garcia De Leaniz
Sofia Consuegra del Olmo
author2 Tamsyn Uren Webster
Sofia Consuegra
Matthew Hitchings
Carlos Garcia De Leaniz
Sofia Consuegra del Olmo
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container_title Applied and Environmental Microbiology
container_volume 84
container_issue 16
publishDate 2018
institution Swansea University
issn 0099-2240
1098-5336
doi_str_mv 10.1128/AEM.00691-18
publisher American Society for Microbiology
college_str Faculty of Science and Engineering
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hierarchy_top_title Faculty of Science and Engineering
hierarchy_parent_id facultyofscienceandengineering
hierarchy_parent_title Faculty of Science and Engineering
department_str School of Biosciences, Geography and Physics - Biosciences{{{_:::_}}}Faculty of Science and Engineering{{{_:::_}}}School of Biosciences, Geography and Physics - Biosciences
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description The microbiome has a crucial influence on host phenotype, and is of broad interest to ecological and evolutionary research. Yet, the extent of variation that occurs in the microbiome within and between populations is unclear. We characterised the skin and gut microbiome of seven populations of juvenile Atlantic salmon (Salmo salar) inhabiting a diverse range of environments, including hatchery-reared and wild populations. We found shared skin OTUs across all populations and core gut microbiota for all wild fish, but the diversity and structure of both skin and gut microbial communities were distinct between populations. There was a marked difference between the gut microbiome of wild and captive fish. Hatchery-reared fish had lower intestinal microbial diversity, lacked core microbiota found in wild fish, and showed altered community structure and function. Captive fish skin and gut microbiomes were also less variable within populations, reflecting more uniform artificial rearing conditions. Surrounding water influenced the microbiome of the gut and, especially, the skin, but could not explain the degree of variation observed between populations. For both the gut and skin, we found that there was greater difference in microbial community structure between more genetically distinct fish populations, and also that population genetic diversity was positively correlated with microbiome diversity. However, diet is likely to be the major factor contributing to the large differences in gut microbiota between wild and captive fish. Our results highlight the scope of inter-population variation in the Atlantic salmon microbiome, and offer insights into the deterministic factors contributing to this.
published_date 2018-08-31T03:51:58Z
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