Characterization of the microbiome along the gastrointestinal tracts of semi-artificially reared bar-headed geese (Anser indicus).

As one of the dominant waterfowl species of wetland areas in the Qinghai-Tibet Plateau, since 2003, artificial rearing of bar-headed geese (Anser indicus) has increased in several provinces of China for the purpose of conservation and economic development. In this study, we systematically characterized the microbial community diversity, compositions and predicted functions of semi-artificially reared bar-headed geese by sampling five different gut locations (the oropharynxs, crops, gizzards, ceca, and cloacae) along the gastrointestinal tracts of three individuals. Alpha diversity analyses showed that the gizzards had the richest species diversity and that the ceca had the least. Beta diversity analyses showed that the cecal samples formed their own cluster, while samples from the oropharynxs, crops, gizzards, and cloacae overlapped with each other. At the phylum level, Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, and Fusobacteria constituted the top five dominant phyla among all five gastrointestinal sections. At the genus level, a total of 10 genera with proportions above 2.5% were found to be significantly different among the gastrointestinal sections. Furthermore, 53 genera were detected in all gastrointestinal sections of bar-headed geese. PICRUSt data also predicted a group of microbial functions overrepresented in the different segments of the gastrointestinal tracts. Understanding the microbiota along the bar-headed geese gastrointestinal tracts is essential for future microbiological study of this bird and may contribute to the development of geese husbandry.