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To investigate the community structure and species composition of intestinal microbiota in  Coilia ectenes , sixty-seven samples were collected from Lake Taihu in China. The intestinal microbiota of the  C .  ectenes  were identified by the V4 of the 16S ribosomal RNA gene using high-throughput sequencing. Furthermore, the water quality of different sampling sites was also evaluated. A total of 53 phyla and 730 classified genera were found in all the samples. The eight dominant phyla Planctomycetes, Firmicutes, Proteobacteria, Bacteroidetes, Cyanobacteria, Crenarchaeota, Actinobacteria, and Verrucomicrobia were included. The intestinal microbiota compositions of the  C .  ectenes  obtained from the same location presented more similar profiles, and the intestinal microbiota compositions of the  C .  ectenes  from different geographical locations showed considerable differences. The operational taxonomic units (OTUs) abundance of the intestinal microbiota was significantly correlated with both the concentrations of total nitrogen and chlorophyll-a of the aquatic environment ( p &lt;0.05). Geographical location was an important determinant for the fish’s intestinal microbiota composition. The intestinal microbiota of  C .  ectenes  would be affected by the concentrations of total nitrogen and chlorophyll-a in the water. These findings achieve a basic understanding of fish’s gut microbiota, and are helpful for the protection of fish resources in Lake Taihu and provided the cornerstone to sustainable utlization of  C .  ectenes .

Diversity of Intestinal Microbiota in Coilia ectenes from Lake Taihu, China