Structure, variation, and assembly of body-wide microbiomes in endangered crested ibis Nipponia nippon

Limited knowledge of bird microbiome in the all-body niche hinders our understanding of host–microbial relationships and animal health. Here, we characterized the microbial composition of the crested ibis from 13 body sites, representing the cloaca, oral, feather, and skin habitats, and explored assembly mechanism structuring the bacterial community of the four habitats, respectively. The bacterial community characteristics were distinct among the four habitats. The skin harbored the highest alpha diversity, most diverse functions, and more complex network, followed by feather, oral, and cloaca. Individual-specific features were observed when the skin and feathers were concentrated independently. Skin and feather samples of multiple body sites from the same individual were more similar than those from different individuals. Although a significant proportion of the microbiota in the host (3.5% to 14.5%) was not derived from the environmental microbiome, as body sites became more exposed to the environment, the relative importance of neutral processes increased. Neutral processes were the most important contributor in shaping the feather microbiome communities (R2=0.859). A higher percentage of taxa (29.3%) on the skin were selected by hosts compared to taxa on other body habitats. This study demonstrated that niche speciation and partial neutral processes, rather than environmental sources, contribute to microbiome variation in the crested ibis. These results enhance our knowledge of baseline microbial diversity in birds and will aid health management in crested ibises in the future.