A network meta-analysis on comparison of invasive and non-invasive sampling methods to characterize intestinal microbiota of birds

Zhou, Tianlong; Bodawatta, Kasun H.; Jiang, Aiwu

doi:10.1016/j.avrs.2023.100086

Cited by 2 publications

(2 citation statements)

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“…The gut microbiota plays a crucial role in digestion, nutrient metabolism, immune modulation, and overall host well-being [ 35 ]. Captive environments can significantly influence the gut microbiota of birds such as phylogenetic status, diet changes, treatments, and reduced contact with other individuals leading to distinct microbial communities [ 36 , 37 ].…”

Section: Discussionmentioning

confidence: 99%

Gut Fungal Communities Are Influenced by Seasonality in Captive Baikal Teal (Sibirionetta formosa) and Common Teal (Anas crecca)

Sakda,

Xiang,

et al. 2023

Animals

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Understanding the dynamics of avian gut fungal communities and potentially pathogenic species across different seasons is crucial for assessing their health and ecological interactions. In this study, high-throughput sequencing was employed to examine the changes in gut fungal communities and the presence of potential pathogens between different seasons in captive Baikal teal and common teal. Between the summer and autumn seasons, both duck species showed significant differences in fungal diversity and community composition. A higher fungal diversity in both species was exhibited in the summer than in the autumn. Ascomycota and Basidiomycota were the two most common phyla, with a greater proportion of Ascomycota than Basidiomycota in both duck species in the summer. Interestingly, our study also identified animal pathogens and plant saprotrophs in the gut fungal communities. Seasonal variation had an effect on the diversity and abundance of both animal pathogens and saprotrophs. Specifically, during the summer season, the diversity and relative abundance were higher compared to the autumn season. In addition, there were differences between duck species in terms of animal pathogens, while no significant differences were observed in saprotrophs. Overall, the communities of the gut fungi, animal pathogens, and saprotrophs were found to be influenced by seasonal changes rather than host species. Therefore, seasonal variations might dominate over host genetics in shaping the gut microbiota of captive Baikal teal and common teal. This study underscores the importance of incorporating an understanding of seasonal dynamics and potential pathogens within the gut microbiota of captive ducks. Such considerations have the potential to drive progress in the development of sustainable and economically viable farming practices.

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Section: Discussionmentioning

confidence: 99%

Gut Fungal Communities Are Influenced by Seasonality in Captive Baikal Teal (Sibirionetta formosa) and Common Teal (Anas crecca)

Sakda,

Xiang,

et al. 2023

Animals

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“…In fish studies, both techniques have generally been used with prior sacrifice of the animal for gut dissection. However, if the size of the fish is adequate to allow the annal entry of flexible applicators with low thickness, swabbing may be implemented as a quick non-lethal sampling technique in future research studies of the fish gut microbial communities, as is done in higher vertebrates (31)(32)(33). This is of special relevance in the era of animal welfare and the 3Rs (replacement, reduction and refinement) principles in humane animal research, especially under the scopes of reduction and refinement.…”

Section: Introductionmentioning

confidence: 99%

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

Ruiz,

Torrecillas,

Kashinskaya

et al. 2024

Front. Vet. Sci.

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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.

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A network meta-analysis on comparison of invasive and non-invasive sampling methods to characterize intestinal microbiota of birds

Cited by 2 publications

References 85 publications

Gut Fungal Communities Are Influenced by Seasonality in Captive Baikal Teal (Sibirionetta formosa) and Common Teal (Anas crecca)

Gut Fungal Communities Are Influenced by Seasonality in Captive Baikal Teal (Sibirionetta formosa) and Common Teal (Anas crecca)

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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