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...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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Wiley
2019-10-01
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| Series: | MicrobiologyOpen |
| Subjects: | |
| Online Access: | https://doi.org/10.1002/mbo3.898 |
| _version_ | 1819069911493771264 |
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| author | Terje Klemetsen Nils Peder Willassen Christian René Karlsen |
| author_facet | Terje Klemetsen Nils Peder Willassen Christian René Karlsen |
| author_sort | Terje Klemetsen |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-12-21T16:57:34Z |
| format | Article |
| id | doaj.art-c6a27fbde1ec423ba8d12bcb2c475a45 |
| institution | Directory Open Access Journal |
| issn | 2045-8827 |
| language | English |
| last_indexed | 2024-12-21T16:57:34Z |
| publishDate | 2019-10-01 |
| publisher | Wiley |
| record_format | Article |
| series | MicrobiologyOpen |
| spelling | doaj.art-c6a27fbde1ec423ba8d12bcb2c475a452022-12-21T18:56:43ZengWileyMicrobiologyOpen2045-88272019-10-01810n/an/a10.1002/mbo3.898Full‐length 16S rRNA gene classification of Atlantic salmon bacteria and effects of using different 16S variable regions on community structure analysisTerje Klemetsen0Nils Peder Willassen1Christian René Karlsen2Department of Chemistry, Center for Bioinformatics UiT The Arctic University of Norway Tromsø NorwayDepartment of Chemistry, Center for Bioinformatics UiT The Arctic University of Norway Tromsø NorwayDepartment of fish health Nofima NorwayAbstract 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.https://doi.org/10.1002/mbo3.898Atlantic salmonFull‐length 16S rRNA gene sequencemicrobiota |
| spellingShingle | 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 MicrobiologyOpen Atlantic salmon Full‐length 16S rRNA gene sequence microbiota |
| title | 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_short | 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 |
| topic | Atlantic salmon Full‐length 16S rRNA gene sequence microbiota |
| url | https://doi.org/10.1002/mbo3.898 |
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