Intestinal epigenotype of Atlantic salmon (Salmo salar) associates with tenacibaculosis and gut microbiota composition

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Intestinal epigenotype of Atlantic salmon (Salmo salar) associates with tenacibaculosis and gut microbiota composition. / Hansen, Søren B.; Bozzi, Davide; Mak, Sarah S. T.; Clausen, Cecilie G.; Nielsen, Tue K.; Kodama, Miyako; Hansen, Lars H.; Gilbert, M. Thomas P.; Limborg, Morten T.

In: Genomics, Vol. 115, No. 3, 110629, 2023.

Research output: Contribution to journalJournal articleResearchpeer-review

Harvard

Hansen, SB, Bozzi, D, Mak, SST, Clausen, CG, Nielsen, TK, Kodama, M, Hansen, LH, Gilbert, MTP & Limborg, MT 2023, 'Intestinal epigenotype of Atlantic salmon (Salmo salar) associates with tenacibaculosis and gut microbiota composition', Genomics, vol. 115, no. 3, 110629. https://doi.org/10.1016/j.ygeno.2023.110629

APA

Hansen, S. B., Bozzi, D., Mak, S. S. T., Clausen, C. G., Nielsen, T. K., Kodama, M., Hansen, L. H., Gilbert, M. T. P., & Limborg, M. T. (2023). Intestinal epigenotype of Atlantic salmon (Salmo salar) associates with tenacibaculosis and gut microbiota composition. Genomics, 115(3), [110629]. https://doi.org/10.1016/j.ygeno.2023.110629

Vancouver

Hansen SB, Bozzi D, Mak SST, Clausen CG, Nielsen TK, Kodama M et al. Intestinal epigenotype of Atlantic salmon (Salmo salar) associates with tenacibaculosis and gut microbiota composition. Genomics. 2023;115(3). 110629. https://doi.org/10.1016/j.ygeno.2023.110629

Author

Hansen, Søren B. ; Bozzi, Davide ; Mak, Sarah S. T. ; Clausen, Cecilie G. ; Nielsen, Tue K. ; Kodama, Miyako ; Hansen, Lars H. ; Gilbert, M. Thomas P. ; Limborg, Morten T. / Intestinal epigenotype of Atlantic salmon (Salmo salar) associates with tenacibaculosis and gut microbiota composition. In: Genomics. 2023 ; Vol. 115, No. 3.

Bibtex

@article{2ec5d08607c24d39b4c9caab09a8731c,
title = "Intestinal epigenotype of Atlantic salmon (Salmo salar) associates with tenacibaculosis and gut microbiota composition",
abstract = "It remains a challenge to obtain the desired phenotypic traits in aquacultural production of Atlantic salmon, and part of the challenge might come from the effect that host-associated microorganisms have on the fish phenotype. To manipulate the microbiota towards the desired host traits, it is critical to understand the factors that shape it. The bacterial gut microbiota composition can vary greatly among fish, even when reared in the same closed system. While such microbiota differences can be linked to diseases, the molecular effect of disease on host-microbiota interactions and the potential involvement of epigenetic factors remain largely unknown. The aim of this study was to investigate the DNA methylation differences associated with a tenacibaculosis outbreak and microbiota displacement in the gut of Atlantic salmon. Using Whole Genome Bisulfite Sequencing (WGBS) of distal gut tissue from 20 salmon, we compared the genome-wide DNA methylation levels between uninfected individuals and sick fish suffering from tenacibaculosis and microbiota displacement. We discovered >19,000 differentially methylated cytosine sites, often located in differentially methylated regions, and aggregated around genes. The 68 genes connected to the most significant regions had functions related to the ulcerous disease such as epor and slc48a1a but also included prkcda and LOC106590732 whose orthologs are linked to microbiota changes in other species. Although the expression level was not analysed, our epigenetic analysis suggests specific genes potentially involved in host-microbiota interactions and more broadly it highlights the value of considering epigenetic factors in efforts to manipulate the microbiota of farmed fish.",
keywords = "Aquaculture, Atlantic salmon, DNA methylation, Gut dysbiosis, Tenacibaculosis, WGBS",
author = "Hansen, {S{\o}ren B.} and Davide Bozzi and Mak, {Sarah S. T.} and Clausen, {Cecilie G.} and Nielsen, {Tue K.} and Miyako Kodama and Hansen, {Lars H.} and Gilbert, {M. Thomas P.} and Limborg, {Morten T.}",
note = "Publisher Copyright: {\textcopyright} 2023 The Authors",
year = "2023",
doi = "10.1016/j.ygeno.2023.110629",
language = "English",
volume = "115",
journal = "Genomics",
issn = "0888-7543",
publisher = "Academic Press",
number = "3",

}

RIS

TY - JOUR

T1 - Intestinal epigenotype of Atlantic salmon (Salmo salar) associates with tenacibaculosis and gut microbiota composition

AU - Hansen, Søren B.

AU - Bozzi, Davide

AU - Mak, Sarah S. T.

AU - Clausen, Cecilie G.

AU - Nielsen, Tue K.

AU - Kodama, Miyako

AU - Hansen, Lars H.

AU - Gilbert, M. Thomas P.

AU - Limborg, Morten T.

N1 - Publisher Copyright: © 2023 The Authors

PY - 2023

Y1 - 2023

N2 - It remains a challenge to obtain the desired phenotypic traits in aquacultural production of Atlantic salmon, and part of the challenge might come from the effect that host-associated microorganisms have on the fish phenotype. To manipulate the microbiota towards the desired host traits, it is critical to understand the factors that shape it. The bacterial gut microbiota composition can vary greatly among fish, even when reared in the same closed system. While such microbiota differences can be linked to diseases, the molecular effect of disease on host-microbiota interactions and the potential involvement of epigenetic factors remain largely unknown. The aim of this study was to investigate the DNA methylation differences associated with a tenacibaculosis outbreak and microbiota displacement in the gut of Atlantic salmon. Using Whole Genome Bisulfite Sequencing (WGBS) of distal gut tissue from 20 salmon, we compared the genome-wide DNA methylation levels between uninfected individuals and sick fish suffering from tenacibaculosis and microbiota displacement. We discovered >19,000 differentially methylated cytosine sites, often located in differentially methylated regions, and aggregated around genes. The 68 genes connected to the most significant regions had functions related to the ulcerous disease such as epor and slc48a1a but also included prkcda and LOC106590732 whose orthologs are linked to microbiota changes in other species. Although the expression level was not analysed, our epigenetic analysis suggests specific genes potentially involved in host-microbiota interactions and more broadly it highlights the value of considering epigenetic factors in efforts to manipulate the microbiota of farmed fish.

AB - It remains a challenge to obtain the desired phenotypic traits in aquacultural production of Atlantic salmon, and part of the challenge might come from the effect that host-associated microorganisms have on the fish phenotype. To manipulate the microbiota towards the desired host traits, it is critical to understand the factors that shape it. The bacterial gut microbiota composition can vary greatly among fish, even when reared in the same closed system. While such microbiota differences can be linked to diseases, the molecular effect of disease on host-microbiota interactions and the potential involvement of epigenetic factors remain largely unknown. The aim of this study was to investigate the DNA methylation differences associated with a tenacibaculosis outbreak and microbiota displacement in the gut of Atlantic salmon. Using Whole Genome Bisulfite Sequencing (WGBS) of distal gut tissue from 20 salmon, we compared the genome-wide DNA methylation levels between uninfected individuals and sick fish suffering from tenacibaculosis and microbiota displacement. We discovered >19,000 differentially methylated cytosine sites, often located in differentially methylated regions, and aggregated around genes. The 68 genes connected to the most significant regions had functions related to the ulcerous disease such as epor and slc48a1a but also included prkcda and LOC106590732 whose orthologs are linked to microbiota changes in other species. Although the expression level was not analysed, our epigenetic analysis suggests specific genes potentially involved in host-microbiota interactions and more broadly it highlights the value of considering epigenetic factors in efforts to manipulate the microbiota of farmed fish.

KW - Aquaculture

KW - Atlantic salmon

KW - DNA methylation

KW - Gut dysbiosis

KW - Tenacibaculosis

KW - WGBS

U2 - 10.1016/j.ygeno.2023.110629

DO - 10.1016/j.ygeno.2023.110629

M3 - Journal article

C2 - 37100093

AN - SCOPUS:85154574209

VL - 115

JO - Genomics

JF - Genomics

SN - 0888-7543

IS - 3

M1 - 110629

ER -

ID: 346412833