| Summary: | Abstract The avian gut microbiota plays an important role in shaping the health of its host. However, knowledge of gut bacteria in birds lags behind that of other animals. In this study, we investigated the gut bacterial communities of lesser white‐fronted geese (Anser erythropus) wintering at Shengjin Lake and Caizi Lake, China, using high‐throughput sequencing (Illumina MiSeq). Altogether, 1,053,624 high‐quality sequences and 4,405 operational taxonomic units (OTUs) were acquired from 30 fecal samples (15 per lake). The OTUs represented eight phyla and 17 classes from the Caizi Lake samples and seven phyla and 16 classes from the Shengjin Lake samples. Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes were the dominant phyla. The spatial distance and the Chao1, Simpson, and Shannon indices showed that the alpha diversity differed significantly between the samples from both lakes. The phylogenetic tree and heatmap analyses showed that all the Caizi Lake samples were clustered together and all the Shengjin Lake samples were clustered together. These findings suggest that diet may be an important driver of gut microbial community structure in the birds from each lake, and the obvious differentiation in their gut microbial structures may indicate that the bacteria are highly sensitive to food sources at both lakes.
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