Amplicon sequence variants (ASV) of gut pathogens in hooded cranes and domestic geese

Driven by habitat loss from anthropogenic activities, wintering migratory birds forage together with poultry in paddy fields, and thus impose risks of cross transmitting pathogens. To date, there is little evidence for such risks of pathogen transmission between wild birds and poultry. Using the high-throughput sequencing, we report on detected potential pathogens of both wild hooded cranes Grus monacha and sympatric domestic geese Anser anser domesticus during the wintering period and infer the possibility of cross-species pathogen transmission. The results revealed that the number of shared amplicon sequence variants (ASVs) of potential pathogens between the gut microbiota of the two species was low during the early wintering stage (17.2%; 5 ASVs shared) but increased to 56.3% (18 ASVs shared) during the late wintering stage. That is, potential pathogens in the gut microbial communities of the two species became more similar through co-foraging in paddy fields, supporting cross-transmission of pathogens between hooded cranes and domestic geese during the wintering period. Importantly, transmission appeared to be largely from wild hooded cranes to domestic geese, although some potential pathogens may have become specialized to the domestic goose in late wintering stage. Humans are also facing the risks of contracting these potential pathogens from migratory birds through their frequent contact with domestic poultry. It is, therefore, necessary to closely monitor this pathway of pathogen transmission from wild birds to domestic animals and even to humans.