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

BMC Microbiology

Samuel A. M. Martin¹  Andrew S. Brierley²  David E. K. Ferrier²  Adam J. Wyness³  Morag Clinton⁴ 

[1] School of Biological Sciences, University of Aberdeen, AB24 2TZ, Aberdeen, UK;Scottish Oceans Institute, Gatty Marine Laboratory, School of Biology, University of St Andrews, KY16 8LB, St Andrews, Fife, UK;Scottish Oceans Institute, Gatty Marine Laboratory, School of Biology, University of St Andrews, KY16 8LB, St Andrews, Fife, UK;Coastal Research Group, Department of Zoology and Entomology, Rhodes University, 6139, Makhanda (Grahamstown), South Africa;Scottish Oceans Institute, Gatty Marine Laboratory, School of Biology, University of St Andrews, KY16 8LB, St Andrews, Fife, UK;Department of Veterinary Medicine, University of Alaska Fairbanks, 99775, Fairbanks, AK, USA;

关键词: Experimental design;    Sampling methodology;    Gill microbiota;    Microbial assemblages;    Aquaculture;    Atlantic salmon;    Veterinary microbiology;   

DOI  :  10.1186/s12866-021-02374-0

来源: Springer

【 摘 要 】

BackgroundUnderstanding 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.ResultsThe 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.ConclusionsOverall, 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.

【 授权许可】

CC BY