Pathogenic taxa constitute a substantial portion of bat and wild bird fecal bacterial microbiota

Abstract We report European-wide characteristics of fecal bacterial microbiota of four migratory vertebrates. The 351 sample PacBio dataset of almost the entire 16S rRNA gene on one bat (Pipistrellus nathusii) and three bird species (Turdus merula, Anas platyrhynchos, Columba palumbus) with 438,997 amplicon sequence variants assigned 3,277 bacterial species. Plant pathogens were frequently detected, in particular with bat, e.g., Erwinia persicina and Pseudomonas syringae. Also, >90% of the PacBio reads were assigned in 36 samples to genera having species pathogenic to human or animals, e.g., the well-known or emerging enteropathogens Campylobacter jejuni and Escherichia marmotae. We designate individuals of these 36 samples as pathogen bloomers, i.e., previously unknown high risk sources of pathogen spillover. Statistically, more pathogen PacBio reads were detected at higher latitudes and in younger age groups. The studied highly mobile vertebrates appear as a potential concern for human, animal and plant health across the European continent.