Intestinal epigenotype of Atlantic salmon (Salmo salar) associates with tenacibaculosis and gut microbiota composition.
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 criti...
Published in: | Genomics |
---|---|
Main Authors: | , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
2023
|
Subjects: | |
Online Access: | https://serval.unil.ch/notice/serval:BIB_5BEFC9E5466B https://doi.org/10.1016/j.ygeno.2023.110629 |
id |
ftunivlausanne:oai:serval.unil.ch:BIB_5BEFC9E5466B |
---|---|
record_format |
openpolar |
spelling |
ftunivlausanne:oai:serval.unil.ch:BIB_5BEFC9E5466B 2024-02-11T10:02:05+01:00 Intestinal epigenotype of Atlantic salmon (Salmo salar) associates with tenacibaculosis and gut microbiota composition. Hansen, S.B. Bozzi, D. Mak, SST Clausen, C.G. Nielsen, T.K. Kodama, M. Hansen, L.H. Gilbert, MTP Limborg, M.T. 2023-05 https://serval.unil.ch/notice/serval:BIB_5BEFC9E5466B https://doi.org/10.1016/j.ygeno.2023.110629 eng eng info:eu-repo/semantics/altIdentifier/doi/10.1016/j.ygeno.2023.110629 info:eu-repo/semantics/altIdentifier/pmid/37100093 info:eu-repo/semantics/altIdentifier/eissn/1089-8646 https://serval.unil.ch/notice/serval:BIB_5BEFC9E5466B doi:10.1016/j.ygeno.2023.110629 urn:issn:0888-7543 Genomics, vol. 115, no. 3, pp. 110629 Animals Gastrointestinal Microbiome/genetics Salmo salar Bacteria/genetics Microbiota Aquaculture Atlantic salmon DNA methylation Gut dysbiosis Tenacibaculosis WGBS info:eu-repo/semantics/article article 2023 ftunivlausanne https://doi.org/10.1016/j.ygeno.2023.110629 2024-01-22T01:09:10Z 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. Article in Journal/Newspaper Atlantic salmon Salmo salar Université de Lausanne (UNIL): Serval - Serveur académique lausannois Genomics 115 3 110629 |
institution |
Open Polar |
collection |
Université de Lausanne (UNIL): Serval - Serveur académique lausannois |
op_collection_id |
ftunivlausanne |
language |
English |
topic |
Animals Gastrointestinal Microbiome/genetics Salmo salar Bacteria/genetics Microbiota Aquaculture Atlantic salmon DNA methylation Gut dysbiosis Tenacibaculosis WGBS |
spellingShingle |
Animals Gastrointestinal Microbiome/genetics Salmo salar Bacteria/genetics Microbiota Aquaculture Atlantic salmon DNA methylation Gut dysbiosis Tenacibaculosis WGBS Hansen, S.B. Bozzi, D. Mak, SST Clausen, C.G. Nielsen, T.K. Kodama, M. Hansen, L.H. Gilbert, MTP Limborg, M.T. Intestinal epigenotype of Atlantic salmon (Salmo salar) associates with tenacibaculosis and gut microbiota composition. |
topic_facet |
Animals Gastrointestinal Microbiome/genetics Salmo salar Bacteria/genetics Microbiota Aquaculture Atlantic salmon DNA methylation Gut dysbiosis Tenacibaculosis WGBS |
description |
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. |
format |
Article in Journal/Newspaper |
author |
Hansen, S.B. Bozzi, D. Mak, SST Clausen, C.G. Nielsen, T.K. Kodama, M. Hansen, L.H. Gilbert, MTP Limborg, M.T. |
author_facet |
Hansen, S.B. Bozzi, D. Mak, SST Clausen, C.G. Nielsen, T.K. Kodama, M. Hansen, L.H. Gilbert, MTP Limborg, M.T. |
author_sort |
Hansen, S.B. |
title |
Intestinal epigenotype of Atlantic salmon (Salmo salar) associates with tenacibaculosis and gut microbiota composition. |
title_short |
Intestinal epigenotype of Atlantic salmon (Salmo salar) associates with tenacibaculosis and gut microbiota composition. |
title_full |
Intestinal epigenotype of Atlantic salmon (Salmo salar) associates with tenacibaculosis and gut microbiota composition. |
title_fullStr |
Intestinal epigenotype of Atlantic salmon (Salmo salar) associates with tenacibaculosis and gut microbiota composition. |
title_full_unstemmed |
Intestinal epigenotype of Atlantic salmon (Salmo salar) associates with tenacibaculosis and gut microbiota composition. |
title_sort |
intestinal epigenotype of atlantic salmon (salmo salar) associates with tenacibaculosis and gut microbiota composition. |
publishDate |
2023 |
url |
https://serval.unil.ch/notice/serval:BIB_5BEFC9E5466B https://doi.org/10.1016/j.ygeno.2023.110629 |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_source |
Genomics, vol. 115, no. 3, pp. 110629 |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.1016/j.ygeno.2023.110629 info:eu-repo/semantics/altIdentifier/pmid/37100093 info:eu-repo/semantics/altIdentifier/eissn/1089-8646 https://serval.unil.ch/notice/serval:BIB_5BEFC9E5466B doi:10.1016/j.ygeno.2023.110629 urn:issn:0888-7543 |
op_doi |
https://doi.org/10.1016/j.ygeno.2023.110629 |
container_title |
Genomics |
container_volume |
115 |
container_issue |
3 |
container_start_page |
110629 |
_version_ |
1790597971713196032 |