Faecal microbiota and antibiotic resistance genes in migratory waterbirds with contrasting habitat use

Migratory birds may have a vital role in the spread of antimicrobial resistance across habitats and regions, but empirical data remain scarce. We investigated differences gut microbiome composition abundance antibiotic genes (ARGs) faeces from four migratory waterbirds wintering South-West Spain that differ their habitat use. The white stork Ciconia ciconia lesser black-backed gull Larus fuscus are omnivorous opportunistic use highly anthropogenic such as landfills urban areas. greylag goose Anser anser common crane Grus grus herbivores more natural habitats. Fresh 15 individuals each species were analysed to assess bacterial communities using 16S rRNA amplicon-targeted sequencing, quantify Class I integron integrase gene (intI1) well encoding sulfonamides (sul1), beta-lactams (blaTEM, blaKPC blaNDM), tetracyclines (tetW), fluoroquinolones (qnrS), colistin (mcr-1) qPCR. Bacterial richest most diverse. Beta diversity analysis showed segregation faecal between bird species, those storks gulls similar, these being regularly feed landfills. Potential pathogens identified differed significantly with higher relative gulls. Faeces (stork gull) contained ARGs (sul1, blaTEM, tetW). Genes conferring last resort antibiotics carbapenems (blaKPC) only observed These results show reservoirs resistant bacteria suggest disseminate environments (e.g., ricefields or water supplies), thus constitute risk for further wildlife humans.