Research Background
Study Overview
The gut microbiota develops rapidly during early life and can influence host nutrition, metabolism, immune function, and development. However, most knowledge of early microbial assembly comes from humans, laboratory animals, or captive species. Far less is known about how these communities form in free-living wild raptors, whose nests are difficult to access and whose populations are often strictly protected.
A study published in Scientific Reports investigated the gut microbiota of nestlings from two raptor species breeding sympatrically in eastern Poland: the white-tailed eagle (Haliaeetus albicilla) and the lesser spotted eagle (Clanga pomarina).
Although the two species occupy overlapping breeding areas, they differ markedly in parental foraging ecology. White-tailed eagles rely largely on fish and waterbirds, whereas lesser spotted eagles primarily consume small mammals and other terrestrial prey. This natural contrast enabled the researchers to examine how host species identity and trophic ecology relate to microbiota composition during the nest-bound stage.
Study Design
Non-Invasive Microbiome Profiling in the Wild
Fresh fecal samples were collected opportunistically during routine nest monitoring and bird ringing in the 2025 breeding season, without capturing or handling animals specifically for the study. In total, the researchers analyzed 60 samples, comprising 30 nestlings from each species, together with information on nest location, chick body mass, ring number, and prey remains.
Bacterial communities were characterized by sequencing the V3–V4 region of the 16S rRNA gene. The study compared taxonomic composition, within-sample diversity, between-sample community structure, geographic distance effects, and variation among individuals and nests.
The researchers also used PICRUSt2 to infer the functional potential of the microbial communities from the 16S rRNA gene data. These results represent predicted metabolic capabilities rather than direct measurements of microbial genes or metabolic activity.
Research Highlights
Key Findings
Early-Life Microbiota Differed Clearly Between Host Species
The two eagle species displayed markedly different bacterial community structures across multiple analytical measures. White-tailed eagle nestlings were enriched in taxa including Bifidobacteriaceae, Moraxellaceae, and Micrococcaceae, whereas lesser spotted eagle nestlings showed higher relative abundances of Enterococcaceae, Enterobacteriaceae, and Pseudomonadaceae, among other families.
These differences were already evident while the nestlings remained dependent on parental provisioning, indicating that species-associated microbiome differentiation emerges early in development. The contrasting trophic niches of the two hosts provide an important ecological context for these patterns, although the observational study does not isolate diet from other species-specific factors.
Microbial Diversity and Predicted Functions Showed Distinct Patterns
White-tailed eagle nestlings exhibited higher microbial diversity across several alpha-diversity measures, including Shannon diversity, Simpson dominance, Pielou’s evenness, and estimated richness. The between-species separation was also supported by beta-diversity analyses.
Predicted functional profiles differed between the species. The microbiota of white-tailed eagle nestlings showed greater representation of pathways associated with amino acid biosynthesis, whereas the lesser spotted eagle microbiota was enriched in pathways related to carbohydrate degradation and carbon-compound oxidation. Because these functions were inferred from 16S profiles, they should be viewed as hypotheses for future validation through direct functional approaches.
Geographic Effects Were Limited, While Individual Variation Remained High
Geographic distance between nests showed little or no significant relationship with gut microbial dissimilarity. In contrast, substantial variation was observed among individual nestlings, including chicks from the same white-tailed eagle nest, suggesting that individual-specific and potentially stochastic processes contribute to early microbiome assembly.
No dysbiosis-like community profiles were detected in either species. The resulting dataset therefore provides a useful healthy baseline for future studies examining microbiome development, wildlife health, and responses to environmental pressure.
Research Significance
A Baseline for Wildlife Microbiome and Conservation Research
This study provides rare microbiome data from healthy, free-living raptor nestlings sampled under natural conditions. It shows that host species identity is strongly associated with early-life microbial community structure even when the species breed within the same regional landscape.
By combining non-invasive field sampling with microbial community and functional prediction analyses, the research establishes a reference point for future comparisons across developmental stages, populations, and environmental conditions. Longitudinal sampling and direct functional approaches, such as shotgun metagenomics or metatranscriptomics, could further clarify how these early microbial differences develop and whether they influence host health or ecological adaptation.
BMKGENE Contribution
Supporting 16S rRNA Gene Profiling of Wild Raptor Microbiota
BMKGENE provided 16S rRNA gene amplicon sequencing and bioinformatics analysis services for this study. Sequencing of the V3–V4 region generated the data used to characterize bacterial community composition and diversity across the two raptor species.
These services supported the comparison of taxonomic profiles, community diversity, predicted functional potential, and microbiome variation associated with host species, geographic distance, and nest-level factors.
16S rRNA Gene Amplicon Sequencing · Bioinformatics Analysis
Original Publication
Łopucki, R., Stępień-Pyśniak, D., Wójciak, J., et al. Early-life gut microbiota differentiation in sympatric wild raptors. Scientific Reports 16, 20975 (2026). DOI: 10.1038/s41598-026-47288-x.
Post time: Sep-11-2026
