Sampling the fish gill microbiome: a comparison of tissue biopsies and swabs
Abstract Background Understanding the influence of methodology on results is an essential consideration in experimental design. In the expanding field of fish microbiology, many best practices and targeted techniques remain to be refined. This study aimed to compare microbial assemblages obtained fr...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2021-11-01
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| Series: | BMC Microbiology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12866-021-02374-0 |
| _version_ | 1828146849090895872 |
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| author | Morag Clinton Adam J. Wyness Samuel A. M. Martin Andrew S. Brierley David E. K. Ferrier |
| author_facet | Morag Clinton Adam J. Wyness Samuel A. M. Martin Andrew S. Brierley David E. K. Ferrier |
| author_sort | Morag Clinton |
| collection | DOAJ |
| description | Abstract Background Understanding the influence of methodology on results is an essential consideration in experimental design. In the expanding field of fish microbiology, many best practices and targeted techniques remain to be refined. This study aimed to compare microbial assemblages obtained from Atlantic salmon (Salmo salar) gills by swabbing versus biopsy excision. Results demonstrate the variation introduced by altered sampling strategies and enhance the available knowledge of the fish gill microbiome. Results The microbiome was sampled using swabs and biopsies from fish gills, with identical treatment of samples for 16S next generation Illumina sequencing. Results show a clear divergence in microbial communities obtained through the different sampling strategies, with swabbing consistently isolating a more diverse microbial consortia, and suffering less from the technical issue of host DNA contamination associated with biopsy use. Sequencing results from biopsy-derived extractions, however, hint at the potential for more cryptic localisation of some community members. Conclusions Overall, results demonstrate a divergence in the obtained microbial community when different sampling methodology is used. Swabbing appears a superior method for sampling the microbiota of mucosal surfaces for broad ecological research in fish, whilst biopsies might be best applied in exploration of communities beyond the reach of swabs, such as sub-surface and intracellular microbes, as well as in pathogen diagnosis. Most studies on the external microbial communities of aquatic organisms utilise swabbing for sample collection, likely due to convenience. Much of the ultrastructure of gill tissue in live fish is, however, potentially inaccessible to swabbing, meaning swabbing might fail to capture the full diversity of gill microbiota. This work therefore also provides valuable insight into partitioning of the gill microbiota, informing varied applications of different sampling methods in experimental design for future research. |
| first_indexed | 2024-04-11T20:52:03Z |
| format | Article |
| id | doaj.art-88bfe8b3a56a4dfab98c7171c64429b6 |
| institution | Directory Open Access Journal |
| issn | 1471-2180 |
| language | English |
| last_indexed | 2024-04-11T20:52:03Z |
| publishDate | 2021-11-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Microbiology |
| spelling | doaj.art-88bfe8b3a56a4dfab98c7171c64429b62022-12-22T04:03:49ZengBMCBMC Microbiology1471-21802021-11-0121111510.1186/s12866-021-02374-0Sampling the fish gill microbiome: a comparison of tissue biopsies and swabsMorag Clinton0Adam J. Wyness1Samuel A. M. Martin2Andrew S. Brierley3David E. K. Ferrier4Scottish Oceans Institute, Gatty Marine Laboratory, School of Biology, University of St AndrewsScottish Oceans Institute, Gatty Marine Laboratory, School of Biology, University of St AndrewsSchool of Biological Sciences, University of AberdeenScottish Oceans Institute, Gatty Marine Laboratory, School of Biology, University of St AndrewsScottish Oceans Institute, Gatty Marine Laboratory, School of Biology, University of St AndrewsAbstract Background Understanding the influence of methodology on results is an essential consideration in experimental design. In the expanding field of fish microbiology, many best practices and targeted techniques remain to be refined. This study aimed to compare microbial assemblages obtained from Atlantic salmon (Salmo salar) gills by swabbing versus biopsy excision. Results demonstrate the variation introduced by altered sampling strategies and enhance the available knowledge of the fish gill microbiome. Results The microbiome was sampled using swabs and biopsies from fish gills, with identical treatment of samples for 16S next generation Illumina sequencing. Results show a clear divergence in microbial communities obtained through the different sampling strategies, with swabbing consistently isolating a more diverse microbial consortia, and suffering less from the technical issue of host DNA contamination associated with biopsy use. Sequencing results from biopsy-derived extractions, however, hint at the potential for more cryptic localisation of some community members. Conclusions Overall, results demonstrate a divergence in the obtained microbial community when different sampling methodology is used. Swabbing appears a superior method for sampling the microbiota of mucosal surfaces for broad ecological research in fish, whilst biopsies might be best applied in exploration of communities beyond the reach of swabs, such as sub-surface and intracellular microbes, as well as in pathogen diagnosis. Most studies on the external microbial communities of aquatic organisms utilise swabbing for sample collection, likely due to convenience. Much of the ultrastructure of gill tissue in live fish is, however, potentially inaccessible to swabbing, meaning swabbing might fail to capture the full diversity of gill microbiota. This work therefore also provides valuable insight into partitioning of the gill microbiota, informing varied applications of different sampling methods in experimental design for future research.https://doi.org/10.1186/s12866-021-02374-0Experimental designSampling methodologyGill microbiotaMicrobial assemblagesAquacultureAtlantic salmon |
| spellingShingle | Morag Clinton Adam J. Wyness Samuel A. M. Martin Andrew S. Brierley David E. K. Ferrier Sampling the fish gill microbiome: a comparison of tissue biopsies and swabs BMC Microbiology Experimental design Sampling methodology Gill microbiota Microbial assemblages Aquaculture Atlantic salmon |
| title | Sampling the fish gill microbiome: a comparison of tissue biopsies and swabs |
| title_full | Sampling the fish gill microbiome: a comparison of tissue biopsies and swabs |
| title_fullStr | Sampling the fish gill microbiome: a comparison of tissue biopsies and swabs |
| title_full_unstemmed | Sampling the fish gill microbiome: a comparison of tissue biopsies and swabs |
| title_short | Sampling the fish gill microbiome: a comparison of tissue biopsies and swabs |
| title_sort | sampling the fish gill microbiome a comparison of tissue biopsies and swabs |
| topic | Experimental design Sampling methodology Gill microbiota Microbial assemblages Aquaculture Atlantic salmon |
| url | https://doi.org/10.1186/s12866-021-02374-0 |
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