Inter-population variation in the Atlantic salmon microbiome reflects environmental and genetic diversity.

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PubMed ID: 29915104

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Uren Webster TM, Consuegra S, Hitchings M, Garcia de Leaniz C

Appl Environ Microbiol. Jun 2018

COMMENT: 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.

In this article Uren Webster and coworkers 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. They 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. Skin and gut microbiomes were also less variable within captive 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 gut and skin, they found that there was greater difference in microbiome 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.

Their results highlight the scope of inter-population variation in the Atlantic salmon microbiome, and offer insights into the deterministic factors contributing to microbiome diversity and structure.

According to author's oppinion:

Our results offer an insight into how the microbiome could potentially contribute to the generation of local adaptations in this species and how domestication alters intestinal microbial communities, highlighting future research directions in these areas.

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Javier Velasco