Abstract
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.
Highlights
The microbiome is considered critical to health in many aquatic organisms, which requires maintenance of a diverse microbial community [1]
Beyond different collection strategies, sampled material was treated identically to explore the impact of sampling methodology on results (Fig. 1)
Results indicate consistent trends in communities obtained with varied sampling methodology, which is Results support a divergence in data obtained from identically treated swab and biopsy-derived highthroughput sequencing, indicating different sampling methodology likely impacts the microbial genomic
Summary
The microbiome is considered critical to health in many aquatic organisms, which requires maintenance of a diverse microbial community [1]. Study of the Clinton et al BMC Microbiology (2021) 21:313 the microbiota is in homeostasis, whenever this breaks down ‘dysbiosis’ is considered to occur; whereby a disrupted microbiome results as a consequence of, or predisposition to, disease [12,13,14]. Of particular interest to researchers are the relationships between important aquaculture species such as Atlantic salmon (Salmo salar) and their microbial consortia [18, 19]. Many critical uncertainties remain as yet in this area of research, regarding the involvement of microbial communities and other factors that influence the complex suite of gill disorders experienced by these fish [20,21,22,23]. Results demonstrate the variation introduced by altered sampling strategies and enhance the available knowledge of the fish gill microbiome
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