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Whooper Swans in Urban and Natural Xinjiang Wetlands Had Different Gut Microbiomes

Wintering whooper swan in Beijing, China
Research · Disease, parasites & microbiology

Whooper swans (Cygnus cygnus) wintering in an urban wetland and a natural river habitat in Xinjiang, China, had clearly different gut bacterial communities. Researchers analysed 34 fresh faecal samples collected in December 2025: 21 from Swan Bay on the Kaidu River in Hejing County and 13 from Workers’ Park in Korla City, an artificial urban wetland with intensive recreation and regular feeding of swans.

The Two Groups Shared a Microbial Core

Using 16S rRNA gene sequencing — sequencing a bacterial marker gene to identify and compare bacteria in the faecal samples — the researchers identified 2,207 operational taxonomic units, or OTUs—clusters of closely similar bacterial sequences used here to describe microbial types. Of these, 734 occurred in both habitats. The two groups were also dominated by the same major bacterial phyla, including Firmicutes, Fusobacteriota, Proteobacteria, Campylobacterota and Bacteroidota, showing that a substantial core microbiota was shared despite the contrasting winter environments.

The Habitats Differed in the Balance of Bacteria

The balance within that core differed, however. The overall bacterial community structure differed clearly between the two habitats. The urban group also had a higher Simpson diversity index, which the authors interpret mainly as a more even distribution of bacterial taxa rather than a clear increase in the total number of taxa. Other diversity measures did not show a clear difference: Chao1, which mainly estimates how many taxa are present, and Shannon diversity, which combines taxon richness and evenness, showed no clear difference between habitats.

Several bacterial groups also differed in relative abundance. The urban swans had relatively more Campylobacter and Psychrobacter, whereas swans from the natural river habitat had higher relative abundances of groups including Fusobacterium, Romboutsia and Cetobacterium. In the authors’ discussion, several taxa enriched in the natural-river group are linked by earlier research to nutrient fermentation and short-chain-fatty-acid production, while the urban group contained more environmentally associated taxa. These are habitat-associated patterns: the study does not show that the habitat itself directly caused the microbial differences or that they produced a particular health effect.

Predicted Functions Pointed to Metabolic Differences

The researchers also used PICRUSt2 to infer likely microbial functions from the 16S profiles. This analysis predicted stronger representation of several metabolism-related pathways in the natural-river group, including pathways linked to carbohydrate and short-chain-fatty-acid metabolism. These are predictions from bacterial sequence data, not direct measurements of metabolic activity.

Free-Ranging Samples Limit Causal Conclusions

Because the samples came from free-ranging birds, the researchers could not control for sex, age, body condition or individual diet. They therefore describe the results as a preliminary baseline and recommend future work using methods such as metagenomics, dietary analyses and direct pathogen testing to determine what the microbiome differences mean for swan physiology and health.

Sources and image credit

  1. Gut Microbiota Composition and Predicted Functional Profiles: Functional Adaptation of Overwintering Whooper Swans (Cygnus cygnus) Across Habitats with Contrasting Anthropogenic DisturbancePrimary open-access study published 23 August 2026. Researchers analysed 34 fresh fecal samples from whooper swans wintering at natural Swan Bay in Hejing County (n=21) and urban Workers’ Park in Korla City (n=13), Xinjiang. They identified 2,207 OTUs, 734 shared between habitats. The urban group had a significantly higher Simpson index while Chao1 and Shannon did not differ significantly; weighted and unweighted UniFrac analyses showed significant differences in community structure. PICRUSt2 predicted greater enrichment of metabolism-related pathways in the natural-river group, but the authors stress these are functional predictions rather than direct metabolic measurements and note limitations from non-invasive sampling of unidentified individuals.

Image: 星外之神 — wintering Whooper Swan in Yuanmingyuan, Beijing, China, photographed 17 January 2026; Wikimedia Commons. Representative Chinese wintering image, not a bird from the Xinjiang study. · CC BY-SA 4.0 · Source

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