Abstract: This study aimed to understand the intestinal microbial diversity and community structure of wild cold-water fishes in Eerqisi River in Altay region, Xinjiang, China. The V4 region of the 16S rRNA gene was sequenced by high-throughput sequencing and the microbial community compositions in the intestinal contents and mucosa of three kinds of cold-water fish were compared. A total of 58 328 effective sequences and 242 operational taxonomic units (OTUs) were obtained. Diversity analysis indicated that the Shannon index in Hucho taimen was lower than those in Qinling lenok and Esox reicherti. The microbial community structure of Qinling lenok was closer to that of Esox reicherti. At the phylum level, Firmicutes and Gammaproteobacteria dominated the microbiota of six fish samples. Firmicutes was the most dominant phylum in Hucho taimen samples. However, Gammaproteobacteria was increased significantly in Qinling lenok and Esox reicherti, whereas Firmicutes was decreased sharply. At the genus level, Carnobacterium was the most abundant in Hucho taimen. Psychrobacter, Acinetobacter and Clostridium sensu stricto were the main microbial populations in both Qinling lenok and Esox reicherti. Marked differences were detected in the microbial community composition and diversity of different cold-water fishes, while for the same fish the microbial community composition in the intestinal contents and mucosa was similar, without significant differences.

Key words: cold-water fishes, microbial diversity, high-throughput sequencing