The gut microbiome of farmed Arctic char (Salvelinus alpinus) is shaped by feeding stage and nutrient presence
The gut microbiome plays an important role in maintaining health and productivity of farmed fish. However, the functional role of most gut microorganisms remains unknown. Identifying the stable members of the gut microbiota and understanding their functional roles could aid in the selection of posit...
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Language: | English |
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Oxford University Press (OUP)
2024
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Online Access: | https://archimer.ifremer.fr/doc/00888/100021/110249.pdf https://archimer.ifremer.fr/doc/00888/100021/110250.zip https://doi.org/10.1093/femsmc/xtae011 https://archimer.ifremer.fr/doc/00888/100021/ |
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ftarchimer:oai:archimer.ifremer.fr:100021 2024-06-23T07:49:32+00:00 The gut microbiome of farmed Arctic char (Salvelinus alpinus) is shaped by feeding stage and nutrient presence Knobloch, Stephen Skirnisdóttir, Sigurlaug Dubois, Marianne Mayolle, Lucie Kolypczuk, Laetitia Leroi, Francoise Leeper, Alexandra Passerini, Delphine Marteinsson, Viggó Þ 2024-04-23 application/pdf https://archimer.ifremer.fr/doc/00888/100021/110249.pdf https://archimer.ifremer.fr/doc/00888/100021/110250.zip https://doi.org/10.1093/femsmc/xtae011 https://archimer.ifremer.fr/doc/00888/100021/ eng eng Oxford University Press (OUP) info:eu-repo/grantAgreement/EC/H2020/818368/EU//MASTER https://archimer.ifremer.fr/doc/00888/100021/110249.pdf https://archimer.ifremer.fr/doc/00888/100021/110250.zip doi:10.1093/femsmc/xtae011 https://archimer.ifremer.fr/doc/00888/100021/ info:eu-repo/semantics/openAccess restricted use FEMS Microbes (2633-6685) (Oxford University Press (OUP)), 2024-04-23 , Vol. 5 , P. xtae011 (13p.) Aquaculture gut microbiome Arctic char salmon Mycoplasma Ruminococcaceae metagenomics text Article info:eu-repo/semantics/article 2024 ftarchimer https://doi.org/10.1093/femsmc/xtae011 2024-05-29T00:00:22Z The gut microbiome plays an important role in maintaining health and productivity of farmed fish. However, the functional role of most gut microorganisms remains unknown. Identifying the stable members of the gut microbiota and understanding their functional roles could aid in the selection of positive traits or act as a proxy for fish health in aquaculture. Here, we analyse the gut microbial community of farmed juvenile Arctic char (Salvelinus alpinus) and reconstruct the metabolic potential of its main symbionts. The gut microbiota of Arctic char undergoes a succession in community composition during the first weeks post hatch, with a decrease in Shannon diversity and the establishment of three dominant bacterial taxa. The genome of the most abundant bacterium, a Mycoplasma sp., shows adaptation to rapid growth in the nutrient rich gut environment. The second most abundant taxon, a Brevinema sp., has versatile metabolic potential, including genes involved in host mucin degradation and utilisation. However, during periods of absent gut content, a Ruminococcaceae bacterium becomes dominant, possibly outgrowing all other bacteria through the production of secondary metabolites involved in quorum sensing and cross-inhibition while benefiting the host through short-chain fatty acid production. Whereas Mycoplasma is often present as a symbiont in farmed salmonids, we show that the Ruminococcaceae species is also detected in wild Arctic char, suggesting a close evolutionary relationship between the host and this symbiotic bacterium. Article in Journal/Newspaper Arctic Salvelinus alpinus Archimer (Archive Institutionnelle de l'Ifremer - Institut français de recherche pour l'exploitation de la mer) Arctic FEMS Microbes 5 |
institution |
Open Polar |
collection |
Archimer (Archive Institutionnelle de l'Ifremer - Institut français de recherche pour l'exploitation de la mer) |
op_collection_id |
ftarchimer |
language |
English |
topic |
Aquaculture gut microbiome Arctic char salmon Mycoplasma Ruminococcaceae metagenomics |
spellingShingle |
Aquaculture gut microbiome Arctic char salmon Mycoplasma Ruminococcaceae metagenomics Knobloch, Stephen Skirnisdóttir, Sigurlaug Dubois, Marianne Mayolle, Lucie Kolypczuk, Laetitia Leroi, Francoise Leeper, Alexandra Passerini, Delphine Marteinsson, Viggó Þ The gut microbiome of farmed Arctic char (Salvelinus alpinus) is shaped by feeding stage and nutrient presence |
topic_facet |
Aquaculture gut microbiome Arctic char salmon Mycoplasma Ruminococcaceae metagenomics |
description |
The gut microbiome plays an important role in maintaining health and productivity of farmed fish. However, the functional role of most gut microorganisms remains unknown. Identifying the stable members of the gut microbiota and understanding their functional roles could aid in the selection of positive traits or act as a proxy for fish health in aquaculture. Here, we analyse the gut microbial community of farmed juvenile Arctic char (Salvelinus alpinus) and reconstruct the metabolic potential of its main symbionts. The gut microbiota of Arctic char undergoes a succession in community composition during the first weeks post hatch, with a decrease in Shannon diversity and the establishment of three dominant bacterial taxa. The genome of the most abundant bacterium, a Mycoplasma sp., shows adaptation to rapid growth in the nutrient rich gut environment. The second most abundant taxon, a Brevinema sp., has versatile metabolic potential, including genes involved in host mucin degradation and utilisation. However, during periods of absent gut content, a Ruminococcaceae bacterium becomes dominant, possibly outgrowing all other bacteria through the production of secondary metabolites involved in quorum sensing and cross-inhibition while benefiting the host through short-chain fatty acid production. Whereas Mycoplasma is often present as a symbiont in farmed salmonids, we show that the Ruminococcaceae species is also detected in wild Arctic char, suggesting a close evolutionary relationship between the host and this symbiotic bacterium. |
format |
Article in Journal/Newspaper |
author |
Knobloch, Stephen Skirnisdóttir, Sigurlaug Dubois, Marianne Mayolle, Lucie Kolypczuk, Laetitia Leroi, Francoise Leeper, Alexandra Passerini, Delphine Marteinsson, Viggó Þ |
author_facet |
Knobloch, Stephen Skirnisdóttir, Sigurlaug Dubois, Marianne Mayolle, Lucie Kolypczuk, Laetitia Leroi, Francoise Leeper, Alexandra Passerini, Delphine Marteinsson, Viggó Þ |
author_sort |
Knobloch, Stephen |
title |
The gut microbiome of farmed Arctic char (Salvelinus alpinus) is shaped by feeding stage and nutrient presence |
title_short |
The gut microbiome of farmed Arctic char (Salvelinus alpinus) is shaped by feeding stage and nutrient presence |
title_full |
The gut microbiome of farmed Arctic char (Salvelinus alpinus) is shaped by feeding stage and nutrient presence |
title_fullStr |
The gut microbiome of farmed Arctic char (Salvelinus alpinus) is shaped by feeding stage and nutrient presence |
title_full_unstemmed |
The gut microbiome of farmed Arctic char (Salvelinus alpinus) is shaped by feeding stage and nutrient presence |
title_sort |
gut microbiome of farmed arctic char (salvelinus alpinus) is shaped by feeding stage and nutrient presence |
publisher |
Oxford University Press (OUP) |
publishDate |
2024 |
url |
https://archimer.ifremer.fr/doc/00888/100021/110249.pdf https://archimer.ifremer.fr/doc/00888/100021/110250.zip https://doi.org/10.1093/femsmc/xtae011 https://archimer.ifremer.fr/doc/00888/100021/ |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic Salvelinus alpinus |
genre_facet |
Arctic Salvelinus alpinus |
op_source |
FEMS Microbes (2633-6685) (Oxford University Press (OUP)), 2024-04-23 , Vol. 5 , P. xtae011 (13p.) |
op_relation |
info:eu-repo/grantAgreement/EC/H2020/818368/EU//MASTER https://archimer.ifremer.fr/doc/00888/100021/110249.pdf https://archimer.ifremer.fr/doc/00888/100021/110250.zip doi:10.1093/femsmc/xtae011 https://archimer.ifremer.fr/doc/00888/100021/ |
op_rights |
info:eu-repo/semantics/openAccess restricted use |
op_doi |
https://doi.org/10.1093/femsmc/xtae011 |
container_title |
FEMS Microbes |
container_volume |
5 |
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1802640017794793472 |