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...

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Autores principales:	Morag Clinton, Adam J. Wyness, Samuel A. M. Martin, Andrew S. Brierley, David E. K. Ferrier
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Experimental design Sampling methodology Gill microbiota Microbial assemblages Aquaculture Atlantic salmon Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/88bfe8b3a56a4dfab98c7171c64429b6
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spelling	oai:doaj.org-article:88bfe8b3a56a4dfab98c7171c64429b62021-11-14T12:08:53ZSampling the fish gill microbiome: a comparison of tissue biopsies and swabs10.1186/s12866-021-02374-01471-2180https://doaj.org/article/88bfe8b3a56a4dfab98c7171c64429b62021-11-01T00:00:00Zhttps://doi.org/10.1186/s12866-021-02374-0https://doaj.org/toc/1471-2180Abstract 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.Morag ClintonAdam J. WynessSamuel A. M. MartinAndrew S. BrierleyDavid E. K. FerrierBMCarticleExperimental designSampling methodologyGill microbiotaMicrobial assemblagesAquacultureAtlantic salmonMicrobiologyQR1-502ENBMC Microbiology, Vol 21, Iss 1, Pp 1-15 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Experimental design Sampling methodology Gill microbiota Microbial assemblages Aquaculture Atlantic salmon Microbiology QR1-502
spellingShingle	Experimental design Sampling methodology Gill microbiota Microbial assemblages Aquaculture Atlantic salmon Microbiology QR1-502 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
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.
format	article
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
title	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_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_sort	sampling the fish gill microbiome: a comparison of tissue biopsies and swabs
publisher	BMC
publishDate	2021
url	https://doaj.org/article/88bfe8b3a56a4dfab98c7171c64429b6
work_keys_str_mv	AT moragclinton samplingthefishgillmicrobiomeacomparisonoftissuebiopsiesandswabs AT adamjwyness samplingthefishgillmicrobiomeacomparisonoftissuebiopsiesandswabs AT samuelammartin samplingthefishgillmicrobiomeacomparisonoftissuebiopsiesandswabs AT andrewsbrierley samplingthefishgillmicrobiomeacomparisonoftissuebiopsiesandswabs AT davidekferrier samplingthefishgillmicrobiomeacomparisonoftissuebiopsiesandswabs
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Sampling the fish gill microbiome: a comparison of tissue biopsies and swabs

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