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Early-life gut microbiota differentiation in sympatric wild raptors

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Abstract

The establishment of the gut microbiota during early life plays a crucial role in host physiology and development, yet remains poorly understood under natural conditions, particularly in wild raptors. Limited access to free-living nestlings constrains our understanding of how host species identity, parental trophic ecology (shaping dietary microbial input and nutrient availability), and environmental factors structure early-life microbiota. Here, we investigated the gut microbiota of nestlings of two sympatric raptor species, the white-tailed eagle (Haliaeetus albicilla) and the lesser spotted eagle (Clanga pomarina), which differ in parental foraging ecology (fish/waterbird vs. small mammal-based diet). Using non-invasive fecal sampling during routine ringing, we characterized gut microbiota composition and predicted functional potential, and tested the effects of host species, geographic distance between nests, and within-nest variability. Gut microbiota composition differed markedly between species, with clear separation of microbial communities and higher alpha diversity in white-tailed eagle nestlings. In contrast, geographic distance between nests had a limited influence on microbiome structure, while pronounced inter-individual and within-nest variability was observed, highlighting the importance of individual-specific and potentially stochastic processes during early microbiome assembly. Predicted functional profiles also differed between species, with enrichment of amino acid biosynthesis pathways in white-tailed eagles and carbohydrate-related pathways in lesser spotted eagles. No dysbiosis-like microbiome profiles were detected in either species, providing a baseline for future comparative studies. Overall, our findings demonstrate strong species-level differentiation in early-life gut microbiota in wild raptors, in the context of contrasting trophic ecology, while local environmental variation appears to be of secondary importance.

Data availability

The sequencing data that support the findings of this study are deposited in NCBI under accession number PRJNA1371595 ([https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1371595/](https:/www.ncbi.nlm.nih.gov/bioproject/PRJNA1371595)).

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Acknowledgements

We thank Sylwester Aftyka from the Lubelskie Ornithological Society for his essential contribution to the nest inspection work, and Roksana Kałuża for her dedicated voluntary assistance.

Author information

Authors and Affiliations

  1. Department of Biomedicine and Environmental Research, Faculty of Medicine, The John Paul II Catholic University of Lublin, Konstantynów 1J, Lublin, 20–708, Poland

    Rafał Łopucki & Marceli Pacan

  2. Faculty of Veterinary Medicine, Department of Veterinary Prevention and Avian Diseases, University of Life Sciences in Lublin, Głęboka 30, Lublin, 20–612, Poland

    Dagmara Stępień-Pyśniak

  3. Lubelskie Ornithological Society, Akademicka 13, Lublin, 20–033, Poland

    Janusz Wójciak

  4. Department of Artificial Intelligence, Faculty of Social and Technical Sciences, The John Paul II Catholic University of Lublin, Konstantynów 1 H, Lublin, 20–708, Poland

    Sara Jurczyk

  5. Laboratory of Genomics and Genetics, Faculty of Medicine, The John Paul II Catholic University of Lublin, Konstantynów 1J, Lublin, 20–708, Poland

    Marceli Pacan & Agnieszka Kuźniar

Authors

  1. Rafał Łopucki
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  2. Dagmara Stępień-Pyśniak
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  3. Janusz Wójciak
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  4. Marceli Pacan
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  6. Agnieszka Kuźniar
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Contributions

R.Ł., A.K and D.S.-P. conceived and designed the study. J.W. coordinated field work and supervised nest monitoring and sample collection. J.W. collected fecal samples and field metadata. A.K., and M.P. performed DNA extraction and laboratory analyses. R.Ł., A.K., S.J. and M.P. conducted bioinformatic processing and statistical analyses of microbiome data. R.Ł., A.K. and D.S.-P. interpreted the results. R.Ł., A.K. and D.S.-P. wrote the manuscript. All authors contributed to manuscript revision, read and approved the final version.

Corresponding author

Correspondence to
Dagmara Stępień-Pyśniak.

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The authors declare no competing interests.

Ethical approval

None of the animals were intentionally captured for the purposes of this study. Fresh fecal samples were opportunistically collected during routine monitoring activities, when nestlings were ringed and nests were inspected by an ornithologist from The Lublin Ornithological Society, authorized to perform bird ringing. The nest inspection was part of a comprehensive, long-term monitoring effort focused on the white-tailed eagle and the lesser spotted eagle population.

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Łopucki, R., Stępień-Pyśniak, D., Wójciak, J. et al. Early-life gut microbiota differentiation in sympatric wild raptors.
Sci Rep (2026). https://doi.org/10.1038/s41598-026-47288-x

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  • DOI: https://doi.org/10.1038/s41598-026-47288-x

Keywords

  • 16S rRNA gene
  • Nestlings
  • White-tailed eagle
  • Lesser spotted eagle
  • Conservation biology
  • Dysbiosis

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