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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ftpubmed:oai:pubmedcentral.nih.gov:6813439 2023-05-15T15:31:22+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 2019-07-04 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6813439/ http://www.ncbi.nlm.nih.gov/pubmed/31271529 https://doi.org/10.1002/mbo3.898 en eng John Wiley and Sons Inc. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6813439/ http://www.ncbi.nlm.nih.gov/pubmed/31271529 http://dx.doi.org/10.1002/mbo3.898 © 2019 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd. This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. CC-BY Original Articles Text 2019 ftpubmed https://doi.org/10.1002/mbo3.898 2019-11-03T02:01:09Z 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. Text Atlantic salmon PubMed Central (PMC) MicrobiologyOpen 8 10 |
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Original Articles 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 |
topic_facet |
Original Articles |
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. |
format |
Text |
author |
Klemetsen, Terje Willassen, Nils Peder Karlsen, Christian René |
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 |
publisher |
John Wiley and Sons Inc. |
publishDate |
2019 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6813439/ http://www.ncbi.nlm.nih.gov/pubmed/31271529 https://doi.org/10.1002/mbo3.898 |
genre |
Atlantic salmon |
genre_facet |
Atlantic salmon |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6813439/ http://www.ncbi.nlm.nih.gov/pubmed/31271529 http://dx.doi.org/10.1002/mbo3.898 |
op_rights |
© 2019 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd. This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. |
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CC-BY |
op_doi |
https://doi.org/10.1002/mbo3.898 |
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MicrobiologyOpen |
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10 |
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1766361874071289856 |