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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ftunivtroemsoe:oai:munin.uit.no:10037/15948 2023-05-15T15:30:45+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 https://hdl.handle.net/10037/15948 https://doi.org/10.1002/mbo3.898 eng eng Wiley Open Access The datasets generated and analyzed in this study are available in the BioProject repository at https://www.ncbi.nlm.nih.gov/bioproject/PRJEB28410. Klemetsen, T. (2021). Developing the MAR databases – Augmenting Genomic Versatility of Sequenced Marine Microbiota. (Doctoral thesis). https://hdl.handle.net/10037/23232 . MicrobiologyOpen info:eu-repo/grantAgreement/RCN/RBGRUNPRIM/194050/Norway/Grunnbevilgning Nofima AS// Klemetsen, T., Willassen, N.P. & Karlsen, C.R. (2019). Full‐length 16S rRNA gene classification of Atlantic salmon bacteria and effects of using different 16S variable regions on community structure analysis. MicrobiologyOpen , e898. https://doi.org/10.1002/mbo3.898 FRIDAID 1714840 doi:10.1002/mbo3.898 2045-8827 https://hdl.handle.net/10037/15948 openAccess VDP::Mathematics and natural science: 400::Chemistry: 440 VDP::Matematikk og Naturvitenskap: 400::Kjemi: 440 Atlantic salmon Full‐length 16S rRNA gene sequence microbiot Journal article Tidsskriftartikkel Peer reviewed 2019 ftunivtroemsoe https://doi.org/10.1002/mbo3.898 2021-12-01T23:54:51Z 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 University of Tromsø: Munin Open Research Archive MicrobiologyOpen 8 10 |
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Open Polar |
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University of Tromsø: Munin Open Research Archive |
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ftunivtroemsoe |
language |
English |
topic |
VDP::Mathematics and natural science: 400::Chemistry: 440 VDP::Matematikk og Naturvitenskap: 400::Kjemi: 440 Atlantic salmon Full‐length 16S rRNA gene sequence microbiot |
spellingShingle |
VDP::Mathematics and natural science: 400::Chemistry: 440 VDP::Matematikk og Naturvitenskap: 400::Kjemi: 440 Atlantic salmon Full‐length 16S rRNA gene sequence microbiot 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 |
VDP::Mathematics and natural science: 400::Chemistry: 440 VDP::Matematikk og Naturvitenskap: 400::Kjemi: 440 Atlantic salmon Full‐length 16S rRNA gene sequence microbiot |
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 |
Article in Journal/Newspaper |
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 |
Wiley Open Access |
publishDate |
2019 |
url |
https://hdl.handle.net/10037/15948 https://doi.org/10.1002/mbo3.898 |
genre |
Atlantic salmon |
genre_facet |
Atlantic salmon |
op_relation |
The datasets generated and analyzed in this study are available in the BioProject repository at https://www.ncbi.nlm.nih.gov/bioproject/PRJEB28410. Klemetsen, T. (2021). Developing the MAR databases – Augmenting Genomic Versatility of Sequenced Marine Microbiota. (Doctoral thesis). https://hdl.handle.net/10037/23232 . MicrobiologyOpen info:eu-repo/grantAgreement/RCN/RBGRUNPRIM/194050/Norway/Grunnbevilgning Nofima AS// Klemetsen, T., Willassen, N.P. & Karlsen, C.R. (2019). Full‐length 16S rRNA gene classification of Atlantic salmon bacteria and effects of using different 16S variable regions on community structure analysis. MicrobiologyOpen , e898. https://doi.org/10.1002/mbo3.898 FRIDAID 1714840 doi:10.1002/mbo3.898 2045-8827 https://hdl.handle.net/10037/15948 |
op_rights |
openAccess |
op_doi |
https://doi.org/10.1002/mbo3.898 |
container_title |
MicrobiologyOpen |
container_volume |
8 |
container_issue |
10 |
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1766361210820755456 |