Gastrointestinal microbiota fulfill pivotal roles in providing a host with nutrition and protection from pathogenic microorganisms. Up to date, most microbiota research has focused on humans and other mammals, whereas birds and especially wild birds lag behind. Within the field of the avian gut microbiome, research is heavily biased towards poultry. In this study, we analyzed the gut microbiome of the Eurasian nuthatch (Sitta europaea), using faecal samples of eight nestlings originating from three nuthatch nests in the south of Ghent (Belgium), using Illumina sequencing of the 16S rRNA gene. Relative frequency analysis showed a dominance of Firmicutes and Actinobacteria and to a lesser extent Proteobacteria. Bacteroidetes and other phyla were relatively rare. At higher taxonomic levels, a high degree of inter-individual variation in terms of overall microbiota community structure as well as dominance of certain bacteria was observed, but with a higher similarity for the nestlings sharing the same nest. When comparing the nuthatch faecal microbiome to that of great tit nestlings that were sampled during the same breeding season and in the same forest fragment, differences in the microbial community structure were observed, revealing distinct dissimilarities in the relative abundancy of taxa between the two bird species. This study is the first report on the nuthatch microbiome and serves as a reference study for nuthatch bacterial diversity and can be used for targeted screening of the composition and general functions of the avian gut microbiome.
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The raw sequencing data are available on NCBI under the BioProject ID PRJNA615317.
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We would like to thank the private owners and the Flemish Forest and Nature Agency (ANB) for granting access to their property, and Robbe De Beelde, Bram Sercu, Irene Van Schrojenstein Lantman and Pieter Vantieghem for help with the fieldwork.
This work was supported by the UGent GOA project Scaling up Functional Biodiversity Research: from Individuals to Landscapes and Back (TREEWEB). E. V. and E.G. are supported by the Research Foundation Flanders [FWO Grants 12E6616N/1507119N and 12W8919N, respectively].
Conflict of interest
The authors declare that they have no conflict of interest.
Bird ringing and handling were carried out under license and guidelines of the Belgian Ringing Scheme and the Flemish authorities (Agentschap voor Natuur en Bos; ANB/BL-FF/V15-00034). All trapping and sampling protocols were approved and permitted by the Ethical Committee VIB (the Flanders Institute for Biotechnology) Ghent site (EC2015-023).
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Communicated by Erko Stackebrandt.
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Goossens, E., Boonyarittichaikij, R., Dekeukeleire, D. et al. Exploring the faecal microbiome of the Eurasian nuthatch (Sitta europaea). Arch Microbiol (2021). https://doi.org/10.1007/s00203-021-02195-9
- Wild bird
- Great tit