Comparative analysis of the microbiome of sympatric wintering Bean Geese, Domestic Ducks, humans, and soil at Shengjin Lake of China reveals potential public risk to human health

The gut microbiota of migratory waterbirds is affected by various complex factors, including cross-species transmission, which increases the risk of pathogen spreading among sympatric animals and poses a potential public health risk to humans. In this study, we investigated the microbial communities of wintering Bean Geese (Anser fabalis), Domestic Ducks (A. platyrhynchos domesticus), humans, and soil using high-throughput sequencing of the 16S rRNA gene region in Shengjin Lake, China. In total, 6, 046, 677 clean reads were obtained, representing 41, 119 operational taxonomic units (OTUs) across the four groups. The dominant microbial phyla were the Proteobacteria, Firmicutes, Bacteroidota, and Actinobacteriota. The Sorensen similarity index and alpha and beta diversity results showed that the gut microbial communities of Bean Geese and Domestic Ducks were more similar to those of the other pairs. Network analysis revealed that Faecalibacterium prausnitzii, Pseudomonas fragi, and Bradyrhizobium elkanii were hubs of the three major modules. Fourteen common microbiomes were identified in Bean Geese, Domestic Ducks, humans, and soil in Shengjin Lake. A total of 96 potential pathogens were identified among the four groups, with 20 specific potentially pathogenic microbiomes found in the gut of Bean Geese. Some of these pathogens are responsible for significant financial losses in the poultry industry and pose risks to human health. Klebsiella pneumoniae, Morganella morganii, Escherichia coli, and Ralstonia insidiosa are potential core pathogens found in the four groups at Shengjin Lake that can cause diseases in humans and animals and facilitate cross-species transmission through various media. Therefore, humans are at risk of contracting these pathogens from migratory birds because of their frequent contact with domestic poultry. However, further studies are required to explore the potential pathogenic species and transmission pathways among sympatric wintering Bean Geese, Domestic Ducks, humans, and soil.