Full‐length 16S rRNA gene classification of Atlantic salmon bacteria and effects of using different 16S variable regions on community structure analysis

Understanding fish‐microbial relationships may be of great value for fish producers as fish growth, development and welfare are influenced by the microbial community associated with the rearing systems and fish surfaces. Accurate methods to generate and analyze these microbial communities would be a...

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Published in:MicrobiologyOpen
Main Authors: Klemetsen, Terje, Willassen, Nils Peder, Karlsen, Christian René
Format: Article in Journal/Newspaper
Language:English
Published: 2019
Subjects:
Online Access:http://hdl.handle.net/11250/2608429
https://doi.org/10.1002/mbo3.898
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spelling ftnofima:oai:nofima.brage.unit.no:11250/2608429 2023-05-15T15:31:24+02:00 Full‐length 16S rRNA gene classification of Atlantic salmon bacteria and effects of using different 16S variable regions on community structure analysis Klemetsen, Terje Willassen, Nils Peder Karlsen, Christian René 2019 application/pdf http://hdl.handle.net/11250/2608429 https://doi.org/10.1002/mbo3.898 eng eng urn:issn:2045-8827 http://hdl.handle.net/11250/2608429 https://doi.org/10.1002/mbo3.898 cristin:1714840 MicrobiologyOpen Peer reviewed Journal article 2019 ftnofima https://doi.org/10.1002/mbo3.898 2022-11-18T06:51:00Z Understanding fish‐microbial relationships may be of great value for fish producers as fish growth, development and welfare are influenced by the microbial community associated with the rearing systems and fish surfaces. Accurate methods to generate and analyze these microbial communities would be an important tool to help improve understanding of microbial effects in the industry. In this study, we performed taxonomic classification and determination of operational taxonomic units on Atlantic salmon microbiota by taking advantage of full‐length 16S rRNA gene sequences. Skin mucus was dominated by the genera Flavobacterium and Psychrobacter. Intestinal samples were dominated by the genera Carnobacterium, Aeromonas, Mycoplasma and by sequences assigned to the order Clostridiales. Applying Sanger sequencing on the full‐length bacterial 16S rRNA gene from the pool of 46 isolates obtained in this study showed a clear assignment of the PacBio full‐length bacterial 16S rRNA gene sequences down to the genus level. One of the bottlenecks in comparing microbial profiles is that different studies use different 16S rRNA gene regions. Comparisons of sequence assignments between full‐length and in silico derived variable 16S rRNA gene regions showed different microbial profiles with variable effects between phylogenetic groups and taxonomic ranks. publishedVersion Article in Journal/Newspaper Atlantic salmon Nofima Knowledge Archive (Brage) MicrobiologyOpen 8 10
institution Open Polar
collection Nofima Knowledge Archive (Brage)
op_collection_id ftnofima
language English
description Understanding fish‐microbial relationships may be of great value for fish producers as fish growth, development and welfare are influenced by the microbial community associated with the rearing systems and fish surfaces. Accurate methods to generate and analyze these microbial communities would be an important tool to help improve understanding of microbial effects in the industry. In this study, we performed taxonomic classification and determination of operational taxonomic units on Atlantic salmon microbiota by taking advantage of full‐length 16S rRNA gene sequences. Skin mucus was dominated by the genera Flavobacterium and Psychrobacter. Intestinal samples were dominated by the genera Carnobacterium, Aeromonas, Mycoplasma and by sequences assigned to the order Clostridiales. Applying Sanger sequencing on the full‐length bacterial 16S rRNA gene from the pool of 46 isolates obtained in this study showed a clear assignment of the PacBio full‐length bacterial 16S rRNA gene sequences down to the genus level. One of the bottlenecks in comparing microbial profiles is that different studies use different 16S rRNA gene regions. Comparisons of sequence assignments between full‐length and in silico derived variable 16S rRNA gene regions showed different microbial profiles with variable effects between phylogenetic groups and taxonomic ranks. publishedVersion
format Article in Journal/Newspaper
author Klemetsen, Terje
Willassen, Nils Peder
Karlsen, Christian René
spellingShingle Klemetsen, Terje
Willassen, Nils Peder
Karlsen, Christian René
Full‐length 16S rRNA gene classification of Atlantic salmon bacteria and effects of using different 16S variable regions on community structure analysis
author_facet Klemetsen, Terje
Willassen, Nils Peder
Karlsen, Christian René
author_sort Klemetsen, Terje
title Full‐length 16S rRNA gene classification of Atlantic salmon bacteria and effects of using different 16S variable regions on community structure analysis
title_short Full‐length 16S rRNA gene classification of Atlantic salmon bacteria and effects of using different 16S variable regions on community structure analysis
title_full Full‐length 16S rRNA gene classification of Atlantic salmon bacteria and effects of using different 16S variable regions on community structure analysis
title_fullStr Full‐length 16S rRNA gene classification of Atlantic salmon bacteria and effects of using different 16S variable regions on community structure analysis
title_full_unstemmed Full‐length 16S rRNA gene classification of Atlantic salmon bacteria and effects of using different 16S variable regions on community structure analysis
title_sort full‐length 16s rrna gene classification of atlantic salmon bacteria and effects of using different 16s variable regions on community structure analysis
publishDate 2019
url http://hdl.handle.net/11250/2608429
https://doi.org/10.1002/mbo3.898
genre Atlantic salmon
genre_facet Atlantic salmon
op_source MicrobiologyOpen
op_relation urn:issn:2045-8827
http://hdl.handle.net/11250/2608429
https://doi.org/10.1002/mbo3.898
cristin:1714840
op_doi https://doi.org/10.1002/mbo3.898
container_title MicrobiologyOpen
container_volume 8
container_issue 10
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