PRJNA485732
greater flamingo cloacal microbiome Targeted loci environmental
Homeostasis of an enteric microbial community early in life is likely to have important fitness benefits. In panmictic species, high dispersal rates and vertical parental transfer may homogenize bacterial communities between breeding sites and age classes. Alternatively, strong selection from the local environment may differentiate bacterial communities between breeding sites. In addition, age-specific life history characteristics, such as long-distance dispersal, may differentiate the microbiome between age classes. Here, we analyzed the cloacal bacterial 16S rRNA gene of fledgling greater flamingos, Pheonicopterus roseus, across nine western Mediterranean breeding sites across four breeding seasons (n = 731) and 27 samples of adult birds from a single site. We found significant spatio-temporal variation in cloacal microbiome communities, and spatial effects seemed to have a stronger effect than temporal effects. The spatial and temporal effects were stronger on the absence/presence of individual bacterial sequences than on core microbiome composition. We further found that geographical distance between sampling sites was negatively correlated with fledgling microbiome similarity. However, fledgling microbiome was more similar between breeding sites than between adult and fledgling microbiomes within the same site. Furthermore, we found the genus Corynebacterium, associated with both seasonal fat uptake and migration in previous studies, was much more abundant in high-dispersing fledglings than in more resident adults. Therefore, local environmental selection is differentiating fledgling microbiome communities between sites despite high host dispersal rates. In addition, age-specific factors appear to result in strong differential selection pressure of core enteric microbiome between adults and fledglings, even within the same environment.