Sampling the fish gill microbiome: a comparison of tissue biopsies and swabs

Morag Clinton*, Adam J. Wyness, Samuel A.M. Martin, Andrew S. Brierley, David E.K. Ferrier

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

9 Citations (Scopus)
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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.

Original languageEnglish
Article number313
Number of pages15
JournalBMC Microbiology
Early online date10 Nov 2021
Publication statusPublished - 10 Nov 2021

Bibliographical note

Funding Information:
The research costs of this work were supported by the BBSRC EASTBIO DTP and Marine Alliance for Science and Technology Scotland (MASTS) small grants funding scheme.

The authors would like to thank Scottish Sea Farms (SSF) for the kind facilitation of fieldwork that provided material in this project, particularly the staff at the Loch Spelve facility, and the health team at SSF, particularly Dr. Ralph Bickerdike. Thanks are due as well to Professor Matt Holden and Kerry Pettigrew of the Infection Group within the Biomedical Sciences Research Complex, School of Medicine, University of St Andrews, for assistance within the laboratory, as well as Dr. David Bass at the Centre for Environment Fisheries and Aquaculture Science for helpful proofreading.


  • Aquaculture
  • Atlantic salmon
  • Experimental design
  • Gill microbiota
  • Microbial assemblages
  • Sampling methodology
  • Veterinary microbiology


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