Characterization of mid-intestinal microbiota of farmed Chinook salmon using 16S rRNA gene metabarcoding
With the growing importance of aquaculture worldwide, characterization of the microbiota of high-value aquaculture species and identification of their shifts induced by changes in fish physiology or nutrition is of special interest. Here we report the first 16S rRNA gene metabarcoding survey of the...
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Institut za Bioloska Istrazivanja "Sinisa Stankovic"
2019
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ftunivqespace:oai:espace.library.uq.edu.au:UQ:b3b00ad 2023-05-15T15:32:30+02:00 Characterization of mid-intestinal microbiota of farmed Chinook salmon using 16S rRNA gene metabarcoding Ciric, Milica Waite, David Draper, Jenny Jones, John Brian 2019-01-01 https://espace.library.uq.edu.au/view/UQ:b3b00ad eng eng Institut za Bioloska Istrazivanja "Sinisa Stankovic" doi:10.2298/ABS190402040C issn:0354-4664 orcid:0000-0002-0184-2942 Int13/1 Gut Bacterial Communities Atlantic Salmon Rainbow-Trout Molecular Analysis Salar L ; Fish Diversity Walbaum Shape 1100 Agricultural and Biological Sciences 1300 Biochemistry Genetics and Molecular Biology Journal Article 2019 ftunivqespace https://doi.org/10.2298/ABS190402040C 2020-12-29T01:19:20Z With the growing importance of aquaculture worldwide, characterization of the microbiota of high-value aquaculture species and identification of their shifts induced by changes in fish physiology or nutrition is of special interest. Here we report the first 16S rRNA gene metabarcoding survey of the mid-intestinal bacteria of Chinook salmon (Oncorhynchus tshawytscha), an economically important aquacultured species. The microbiota of 30 farmed Chinook salmon from a single cohort was surveyed using metabarcode profiling of the V3-V4 hypervariable region of the bacterial 16S rRNA gene. Seawater, feed and mid-intestinal samples and controls were sequenced in quadruplicate to assess both biological and technical variation in the microbial profiles. Over 1000 operational taxonomic units were identified within the cohort, providing a first glimpse into the mid-intestinal microbiota of farmed Chinook salmon. The taxonomic distribution of the salmon microbiota was reasonably stable, with around two thirds of individuals dominated by members of the family Vibrionaceae. We anticipate that the workflow presented in this paper could be applied in other aquacultured fish species to capture variation or dysbiosis occurring as a result of changes in feed, health or environmental conditions. Article in Journal/Newspaper Atlantic salmon The University of Queensland: UQ eSpace Archives of Biological Sciences 71 4 577 587 |
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Open Polar |
collection |
The University of Queensland: UQ eSpace |
op_collection_id |
ftunivqespace |
language |
English |
topic |
Gut Bacterial Communities Atlantic Salmon Rainbow-Trout Molecular Analysis Salar L ; Fish Diversity Walbaum Shape 1100 Agricultural and Biological Sciences 1300 Biochemistry Genetics and Molecular Biology |
spellingShingle |
Gut Bacterial Communities Atlantic Salmon Rainbow-Trout Molecular Analysis Salar L ; Fish Diversity Walbaum Shape 1100 Agricultural and Biological Sciences 1300 Biochemistry Genetics and Molecular Biology Ciric, Milica Waite, David Draper, Jenny Jones, John Brian Characterization of mid-intestinal microbiota of farmed Chinook salmon using 16S rRNA gene metabarcoding |
topic_facet |
Gut Bacterial Communities Atlantic Salmon Rainbow-Trout Molecular Analysis Salar L ; Fish Diversity Walbaum Shape 1100 Agricultural and Biological Sciences 1300 Biochemistry Genetics and Molecular Biology |
description |
With the growing importance of aquaculture worldwide, characterization of the microbiota of high-value aquaculture species and identification of their shifts induced by changes in fish physiology or nutrition is of special interest. Here we report the first 16S rRNA gene metabarcoding survey of the mid-intestinal bacteria of Chinook salmon (Oncorhynchus tshawytscha), an economically important aquacultured species. The microbiota of 30 farmed Chinook salmon from a single cohort was surveyed using metabarcode profiling of the V3-V4 hypervariable region of the bacterial 16S rRNA gene. Seawater, feed and mid-intestinal samples and controls were sequenced in quadruplicate to assess both biological and technical variation in the microbial profiles. Over 1000 operational taxonomic units were identified within the cohort, providing a first glimpse into the mid-intestinal microbiota of farmed Chinook salmon. The taxonomic distribution of the salmon microbiota was reasonably stable, with around two thirds of individuals dominated by members of the family Vibrionaceae. We anticipate that the workflow presented in this paper could be applied in other aquacultured fish species to capture variation or dysbiosis occurring as a result of changes in feed, health or environmental conditions. |
format |
Article in Journal/Newspaper |
author |
Ciric, Milica Waite, David Draper, Jenny Jones, John Brian |
author_facet |
Ciric, Milica Waite, David Draper, Jenny Jones, John Brian |
author_sort |
Ciric, Milica |
title |
Characterization of mid-intestinal microbiota of farmed Chinook salmon using 16S rRNA gene metabarcoding |
title_short |
Characterization of mid-intestinal microbiota of farmed Chinook salmon using 16S rRNA gene metabarcoding |
title_full |
Characterization of mid-intestinal microbiota of farmed Chinook salmon using 16S rRNA gene metabarcoding |
title_fullStr |
Characterization of mid-intestinal microbiota of farmed Chinook salmon using 16S rRNA gene metabarcoding |
title_full_unstemmed |
Characterization of mid-intestinal microbiota of farmed Chinook salmon using 16S rRNA gene metabarcoding |
title_sort |
characterization of mid-intestinal microbiota of farmed chinook salmon using 16s rrna gene metabarcoding |
publisher |
Institut za Bioloska Istrazivanja "Sinisa Stankovic" |
publishDate |
2019 |
url |
https://espace.library.uq.edu.au/view/UQ:b3b00ad |
genre |
Atlantic salmon |
genre_facet |
Atlantic salmon |
op_relation |
doi:10.2298/ABS190402040C issn:0354-4664 orcid:0000-0002-0184-2942 Int13/1 |
op_doi |
https://doi.org/10.2298/ABS190402040C |
container_title |
Archives of Biological Sciences |
container_volume |
71 |
container_issue |
4 |
container_start_page |
577 |
op_container_end_page |
587 |
_version_ |
1766362990173487104 |