Closely-related Photobacterium strains comprise the majority of bacteria in the gut of migrating Atlantic cod (Gadus morhua)
Source at https://doi.org/10.1186/s40168-019-0681-y . Background - The population of Atlantic cod ( Gadus morhua ), also known as Northeast Arctic cod, migrating Atlantic cod, or simply “skrei,” lives mainly in the Barents Sea and Svalbard waters and migrates in annual cycles to the Norwegian coast...
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BioMed Central
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ftunivtroemsoe:oai:munin.uit.no:10037/16395 2023-05-15T14:30:32+02:00 Closely-related Photobacterium strains comprise the majority of bacteria in the gut of migrating Atlantic cod (Gadus morhua) Le Doujet, Typhaine De Santi, Concetta Klemetsen, Terje Hjerde, Erik Willassen, Nils Peder Haugen, Peik 2019-04-17 https://hdl.handle.net/10037/16395 https://doi.org/10.1186/s40168-019-0681-y eng eng BioMed Central Microbiome Le Doujet, T., De Santi, C., Klemetsen, T., Hjerde, E., Willassen, N.P. & Haugen, P. (2019). Closely-related Photobacterium strains comprise the majority of bacteria in the gut of migrating Atlantic cod ( Gadus morhua ). Microbiome, 7 (1), 64. https://doi.org/10.1186/s40168-019-0681-y FRIDAID 1693333 doi:10.1186/s40168-019-0681-y 2049-2618 https://hdl.handle.net/10037/16395 openAccess VDP::Mathematics and natural science: 400::Basic biosciences: 470::General microbiology: 472 VDP::Matematikk og Naturvitenskap: 400::Basale biofag: 470::Generell mikrobiologi: 472 Atlantic cod Skrei Piscivorous Microbiota Microbiome Allochthonous Metagenome-assembled genomes (MAGs) Journal article Tidsskriftartikkel Peer reviewed 2019 ftunivtroemsoe https://doi.org/10.1186/s40168-019-0681-y 2021-06-25T17:56:45Z Source at https://doi.org/10.1186/s40168-019-0681-y . Background - The population of Atlantic cod ( Gadus morhua ), also known as Northeast Arctic cod, migrating Atlantic cod, or simply “skrei,” lives mainly in the Barents Sea and Svalbard waters and migrates in annual cycles to the Norwegian coast in order to spawn eggs during late winter. It is the world’s largest population of Atlantic cod, and the population is distinct from the Norwegian coastal cod (or “fjord” cod). Despite the biological, economic, and cultural importance of migrating Atlantic cod, current knowledge on the associated microbiota is very limited. Using shotgun metagenomics and metaproteomics approaches, we present here the gut microbiota, metagenome-assembled genomes (MAGs) of the most abundant bacterial species, DNA-based functional profile, and the metaproteome of Atlantic cod specimens caught at a spawning area in an open ocean outside of Tromsø, Norway. Results - Our analyses identified 268 bacterial families in DNA isolated from feces of 6 individual migrating Atlantic cod. The most abundant family was Vibrionaceae (52%; 83% if unclassified reads are excluded), with Photobacterium (genus) representing the vast majority. The recovery of metagenome-assembled genomes provided further details and suggests that several closely related Photobacterium strains from the Photobacterium phosphoreum clade are the most abundant. A genomic-based functional profiling showed that the most abundant functional subsystems are “Carbohydrates”; “Amino Acids and Derivatives”; “Protein Metabolism”; “Cofactors, Vitamins, Prosthetic, Groups, and Pigments”; and “DNA Metabolism,” which is in agreement with other studies of gut microbiomes of marine organisms. Finally, the MS-based metaproteomic dataset revealed that the functional category “Protein Metabolism” is highly overrepresented (3×) when compared to the genome-based functional profile, which shows that ribosomal proteins are rich in the bacterial cytosol. Conclusion - We present here the first study of bacterial diversity of the gut of migrating Atlantic cod using shotgun sequencing and metagenome-assembled genomes (MAGs). The most abundant bacteria belong to the Photobacterium genus ( Vibrionaceae family). We also constructed functional profiles of the gut microbiome. These may be used in future studies as a platform for mining of commercially interesting cold-active enzymes. Article in Journal/Newspaper Arctic cod Arctic atlantic cod Barents Sea Gadus morhua Northeast Arctic cod Svalbard Tromsø Skrei University of Tromsø: Munin Open Research Archive Arctic Barents Sea Norway Svalbard Tromsø Microbiome 7 1 |
institution |
Open Polar |
collection |
University of Tromsø: Munin Open Research Archive |
op_collection_id |
ftunivtroemsoe |
language |
English |
topic |
VDP::Mathematics and natural science: 400::Basic biosciences: 470::General microbiology: 472 VDP::Matematikk og Naturvitenskap: 400::Basale biofag: 470::Generell mikrobiologi: 472 Atlantic cod Skrei Piscivorous Microbiota Microbiome Allochthonous Metagenome-assembled genomes (MAGs) |
spellingShingle |
VDP::Mathematics and natural science: 400::Basic biosciences: 470::General microbiology: 472 VDP::Matematikk og Naturvitenskap: 400::Basale biofag: 470::Generell mikrobiologi: 472 Atlantic cod Skrei Piscivorous Microbiota Microbiome Allochthonous Metagenome-assembled genomes (MAGs) Le Doujet, Typhaine De Santi, Concetta Klemetsen, Terje Hjerde, Erik Willassen, Nils Peder Haugen, Peik Closely-related Photobacterium strains comprise the majority of bacteria in the gut of migrating Atlantic cod (Gadus morhua) |
topic_facet |
VDP::Mathematics and natural science: 400::Basic biosciences: 470::General microbiology: 472 VDP::Matematikk og Naturvitenskap: 400::Basale biofag: 470::Generell mikrobiologi: 472 Atlantic cod Skrei Piscivorous Microbiota Microbiome Allochthonous Metagenome-assembled genomes (MAGs) |
description |
Source at https://doi.org/10.1186/s40168-019-0681-y . Background - The population of Atlantic cod ( Gadus morhua ), also known as Northeast Arctic cod, migrating Atlantic cod, or simply “skrei,” lives mainly in the Barents Sea and Svalbard waters and migrates in annual cycles to the Norwegian coast in order to spawn eggs during late winter. It is the world’s largest population of Atlantic cod, and the population is distinct from the Norwegian coastal cod (or “fjord” cod). Despite the biological, economic, and cultural importance of migrating Atlantic cod, current knowledge on the associated microbiota is very limited. Using shotgun metagenomics and metaproteomics approaches, we present here the gut microbiota, metagenome-assembled genomes (MAGs) of the most abundant bacterial species, DNA-based functional profile, and the metaproteome of Atlantic cod specimens caught at a spawning area in an open ocean outside of Tromsø, Norway. Results - Our analyses identified 268 bacterial families in DNA isolated from feces of 6 individual migrating Atlantic cod. The most abundant family was Vibrionaceae (52%; 83% if unclassified reads are excluded), with Photobacterium (genus) representing the vast majority. The recovery of metagenome-assembled genomes provided further details and suggests that several closely related Photobacterium strains from the Photobacterium phosphoreum clade are the most abundant. A genomic-based functional profiling showed that the most abundant functional subsystems are “Carbohydrates”; “Amino Acids and Derivatives”; “Protein Metabolism”; “Cofactors, Vitamins, Prosthetic, Groups, and Pigments”; and “DNA Metabolism,” which is in agreement with other studies of gut microbiomes of marine organisms. Finally, the MS-based metaproteomic dataset revealed that the functional category “Protein Metabolism” is highly overrepresented (3×) when compared to the genome-based functional profile, which shows that ribosomal proteins are rich in the bacterial cytosol. Conclusion - We present here the first study of bacterial diversity of the gut of migrating Atlantic cod using shotgun sequencing and metagenome-assembled genomes (MAGs). The most abundant bacteria belong to the Photobacterium genus ( Vibrionaceae family). We also constructed functional profiles of the gut microbiome. These may be used in future studies as a platform for mining of commercially interesting cold-active enzymes. |
format |
Article in Journal/Newspaper |
author |
Le Doujet, Typhaine De Santi, Concetta Klemetsen, Terje Hjerde, Erik Willassen, Nils Peder Haugen, Peik |
author_facet |
Le Doujet, Typhaine De Santi, Concetta Klemetsen, Terje Hjerde, Erik Willassen, Nils Peder Haugen, Peik |
author_sort |
Le Doujet, Typhaine |
title |
Closely-related Photobacterium strains comprise the majority of bacteria in the gut of migrating Atlantic cod (Gadus morhua) |
title_short |
Closely-related Photobacterium strains comprise the majority of bacteria in the gut of migrating Atlantic cod (Gadus morhua) |
title_full |
Closely-related Photobacterium strains comprise the majority of bacteria in the gut of migrating Atlantic cod (Gadus morhua) |
title_fullStr |
Closely-related Photobacterium strains comprise the majority of bacteria in the gut of migrating Atlantic cod (Gadus morhua) |
title_full_unstemmed |
Closely-related Photobacterium strains comprise the majority of bacteria in the gut of migrating Atlantic cod (Gadus morhua) |
title_sort |
closely-related photobacterium strains comprise the majority of bacteria in the gut of migrating atlantic cod (gadus morhua) |
publisher |
BioMed Central |
publishDate |
2019 |
url |
https://hdl.handle.net/10037/16395 https://doi.org/10.1186/s40168-019-0681-y |
geographic |
Arctic Barents Sea Norway Svalbard Tromsø |
geographic_facet |
Arctic Barents Sea Norway Svalbard Tromsø |
genre |
Arctic cod Arctic atlantic cod Barents Sea Gadus morhua Northeast Arctic cod Svalbard Tromsø Skrei |
genre_facet |
Arctic cod Arctic atlantic cod Barents Sea Gadus morhua Northeast Arctic cod Svalbard Tromsø Skrei |
op_relation |
Microbiome Le Doujet, T., De Santi, C., Klemetsen, T., Hjerde, E., Willassen, N.P. & Haugen, P. (2019). Closely-related Photobacterium strains comprise the majority of bacteria in the gut of migrating Atlantic cod ( Gadus morhua ). Microbiome, 7 (1), 64. https://doi.org/10.1186/s40168-019-0681-y FRIDAID 1693333 doi:10.1186/s40168-019-0681-y 2049-2618 https://hdl.handle.net/10037/16395 |
op_rights |
openAccess |
op_doi |
https://doi.org/10.1186/s40168-019-0681-y |
container_title |
Microbiome |
container_volume |
7 |
container_issue |
1 |
_version_ |
1766304370913181696 |