Analysis of intestinal flora and environmental microbial diversity of Takifugu rubripes

Takifugu rubripes (T. rubripes) is marine fish rich in protein and essential amino acids. With the continuous development of T. rubripes farming, intensive aquaculture has increased the infection rate with fish diseases. To explore the relationship between environmental microbial communities and gut microbiota, we sequenced the 16s rRNA gene V3–V4 region of the microorganisms in the aquaculture water and gut flora of T. rubripes. The results indicated 934 operational taxonomic units for T. rubripes gut contents and aquaculture samples. A total of 31 phyla and 498 genera were identified. At the phylum level, except for the phylum Proteobacteria, the dominant phyla in intestinal contents were Firmicutes, Acidobacteria, and Fusobacteria. However, the dominant phyla in water were Actinobacteria, Cyanobacteria, and Patescibacteria. At the genus level, intestinal contents included Photobacterium, Arcobacter, Vibrio, and Ruminococcaceae. The water samples mainly included Clade_Ia, Rhodobacteraceae, Eutreptiella pomquetensis, Lentibacter, Clade_III, and PeM15. Principal component analysis showed that the microbial compositions of samples from the same source were similar. There were significant differences between the intestinal flora and water microorganisms. Therefore, the research results showed the differences between the microbial communities in the intestinal tract and aquaculture water of T. rubripes and the characteristics of the main pathogenic bacteria; this could help guide the environmental regulation and disease prevention of T. rubripes aquaculture.