European eel ( Anguilla anguilla ) GI tract conserves a unique metagenomics profile in the recirculation aquaculture system (RAS)

We studied microbial communities in the gut of European eels ( Anguilla anguilla ) from two commercial recirculation aquaculture system (RAS) farms by the 16S rRNA gene (V4 region) sequence–based assessments. The dominant bacteria were Proteobacteria, Bacteroidetes, Firmicutes, Cyanobacteria, and Fusobacteria among 39 identified phyla. According to α-diversity indexes, eels from Farm-1 harbored a significantly higher and different microbial abundance than Farm-2 ( p <0.05), indicating eels from individual farm have distinctive gut microbiota with different bacterial abundance and metabolic profile. The gut bacterial community of Farm-2 was altered significantly with the microbiota of supplied feed and contiguous water. In the RAS environment, host physiology itself and rearing conditions jointly affect the eel’s major intestinal microbiota formation. Furthermore, principal coordinate analysis revealed that eel gut microbiome from different farms constitute clusters independently while the gut bacteria were not influenced by RAS water (TW). LEfSe showed that Pseudomonas , Aeromonas , Lactobacillus , and Empedobacter were differentially dominant in Farm-1, but Cetobacterium , Vibrio , and Phyllobacterium were differentially dominant in Farm-2. Our findings shed new light on the in-depth characterization of eel gut microbiota and its association with the RAS farm environment and explored the abundant gut bacteria’s possible function.