Variations of gut microbiota in the wintering black-necked crane (Grus nigricollis) at local and regional scales and its management implications

The composition of gut microbiota (and its dynamic) strongly influences the host organism’s health, and has been reported to be influenced by a variety of intrinsic and extrinsic factors in wild birds. However, most of the studies were carried out on a single geographical scale. A study incorporating comparison on multiple geographic scales should further improve our understanding of the contributing factors for avian gut microbiota. In this study, we compared the composition, diversity and function of gut microbiota among seven sub-divided populations of the black-necked crane (Grus nigricollis) wintering in Caohai wetland, China. Sequences on the V3-V4 region of 16 S rRNA were analyzed and compared to those of birds from the same breeding area, but distant wintering area in Dashanbao wetland. We observed microbiota divergences both within the Caohai wetland and between the two wetlands. Interestingly, the divergences between the two wetlands were much more pronounced than those within the Caohai wetland, strongly suggesting the determining effect of the external factors in this species. Core gut microbial operational taxonomic units were from the phyla Firmicutes, Proteobacteria, and Actinobacteria, which may be closely related in terms of dietary intake. Most importantly, we detected abundant potentially pathogenic bacteria in the Caohai wetland, which require monitoring efforts to avoid cross-species transmission between the birds and local poultry, livestock and residents. We further speculated that the shrinking of foraging grounds, with the resultant shortage of plant foods, led to an increase in fish-eating frequency in this species. We suggested that encouraging farmers to return to the wetland to grow agricultural plants would likely be a good solution.