Comparative study of the gut microbial communities collected by scraping and swabbing in a fish model: a comprehensive guide to promote non-lethal procedures for gut microbial studies
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Autor/a
Kashinskaya, Elena
Solovyev, Mikhail
Fecha de publicación
2024-03-22ISSN
2297-1769
Resumen
In the present study, we propose the use of swabs in non-lethal sampling procedures to collect the mucosa-adhered gut microbiota from the posterior intestine of fish, and therefore, we compare the bacterial communities collected by conventional scraping and by swabbing methods. For this purpose, samples of the posterior intestine of rainbow trout (Oncorhynchus mykiss) were collected first using the swabbing approach, and after fish euthanasia, by mucosa scraping. Finally, bacterial communities were compared by 16S rRNA gene Illumina sequencing. Results from the current study revealed that similar values of bacterial richness and diversity were found for both sampling procedures. Similarly, there were no differences between procedures when using qualitative metrics (Jaccard and unweighted UniFrac) for estimating inter-individual diversity, but the quantitative metrics (Bray-Curtis and weighted UniFrac) showed a higher dispersion when samples were obtained by swabbing compared to scraping. In terms of bacterial composition, there were differences in abundance for the phyla Firmicutes and Proteobacteria. The cause of these differential abundances may be the inability of the swab to access to certain areas, such as the basal region of the intestinal villi. Moreover, swabbing allowed a higher representation of low abundant taxa, which may also have an important role in host microbiome regardless of their low abundance. Overall, our results demonstrate that the sampling method is a factor to be considered in experimental design when studying gut bacterial communities to avoid potential biases in the interpretation or comparison of results from different studies. In addition, the advantages and disadvantages of each procedure (swabbing vs scraping) are discussed in detail, concluding that swabbing can be implemented as a reliable and non-lethal procedure for posterior gut microbiota studies, which is of particular interest for animal welfare and the 3Rs principle, and may offer a wide range of novel applications.
Tipo de documento
Artículo
Versión del documento
Versión publicada
Lengua
English
Materias (CDU)
637 - Productos de los animales domésticos, de la caza y de la pesca
Páginas
12
Publicado por
Frontiers
Publicado en
Frontiers in Veterinary Science
Citación
Ruiz, Alberto, Silvia Torrecillas, Elena N. Kashinskaya, Karl B. Andrée, Mikhail Solovyev, and Enric Gisbert. 2024. “Comparative Study of the Gut Microbial Communities Collected by Scraping and Swabbing in a Fish Model: A Comprehensive Guide to Promote Non-lethal Procedures for Gut Microbial Studies.” Frontiers in Veterinary Science 11. https://doi.org/10.3389/fvets.2024.1374803.
Número del acuerdo de la subvención
MICINN/Plan Estatal de Investigación, Científica, Técnica y de Innovación 2021-2023/TED2021-132054B-C21/ES/Promoting circular economy by the assessment and validation of mushroom industry by-products as sustainable ingredients for diets in swine livestock and fish aquaculture species/GreenBlueCircle
MICINN/Programa Estatal para desarrollar, atraer y retener talento/RYC2021-031414-I/ES/ /
Program
Aqüicultura
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