Full‐length 16S rRNA gene classification of Atlantic salmon bacteria and effects of using different 16S variable regions on community structure analysis
Abstract 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 w...
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ftdoajarticles:oai:doaj.org/article:c6a27fbde1ec423ba8d12bcb2c475a45 2023-05-15T15:30:44+02:00 Full‐length 16S rRNA gene classification of Atlantic salmon bacteria and effects of using different 16S variable regions on community structure analysis Terje Klemetsen Nils Peder Willassen Christian René Karlsen 2019-10-01T00:00:00Z https://doi.org/10.1002/mbo3.898 https://doaj.org/article/c6a27fbde1ec423ba8d12bcb2c475a45 EN eng Wiley https://doi.org/10.1002/mbo3.898 https://doaj.org/toc/2045-8827 2045-8827 doi:10.1002/mbo3.898 https://doaj.org/article/c6a27fbde1ec423ba8d12bcb2c475a45 MicrobiologyOpen, Vol 8, Iss 10, Pp n/a-n/a (2019) Atlantic salmon Full‐length 16S rRNA gene sequence microbiota Microbiology QR1-502 article 2019 ftdoajarticles https://doi.org/10.1002/mbo3.898 2022-12-31T12:19:06Z Abstract 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. Article in Journal/Newspaper Atlantic salmon Directory of Open Access Journals: DOAJ Articles MicrobiologyOpen 8 10 |
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Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Atlantic salmon Full‐length 16S rRNA gene sequence microbiota Microbiology QR1-502 |
spellingShingle |
Atlantic salmon Full‐length 16S rRNA gene sequence microbiota Microbiology QR1-502 Terje Klemetsen Nils Peder Willassen Christian René Karlsen Full‐length 16S rRNA gene classification of Atlantic salmon bacteria and effects of using different 16S variable regions on community structure analysis |
topic_facet |
Atlantic salmon Full‐length 16S rRNA gene sequence microbiota Microbiology QR1-502 |
description |
Abstract 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. |
format |
Article in Journal/Newspaper |
author |
Terje Klemetsen Nils Peder Willassen Christian René Karlsen |
author_facet |
Terje Klemetsen Nils Peder Willassen Christian René Karlsen |
author_sort |
Terje Klemetsen |
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 |
publisher |
Wiley |
publishDate |
2019 |
url |
https://doi.org/10.1002/mbo3.898 https://doaj.org/article/c6a27fbde1ec423ba8d12bcb2c475a45 |
genre |
Atlantic salmon |
genre_facet |
Atlantic salmon |
op_source |
MicrobiologyOpen, Vol 8, Iss 10, Pp n/a-n/a (2019) |
op_relation |
https://doi.org/10.1002/mbo3.898 https://doaj.org/toc/2045-8827 2045-8827 doi:10.1002/mbo3.898 https://doaj.org/article/c6a27fbde1ec423ba8d12bcb2c475a45 |
op_doi |
https://doi.org/10.1002/mbo3.898 |
container_title |
MicrobiologyOpen |
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8 |
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10 |
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1766361193705897984 |