Microbiota in monocultured Litopenaeus vannamei vs. polyculture with Trachinotus ovatus

The structures of the microbial community in the intestine, aquaculture water, and sediment of Litopenaeus vannamei, both in monoculture and mixed culture with Trachinotus ovatus, were analyzed by sequencing 16S rRNA amplicons. 1,120,500 valid reads were obtained from 21 samples, and 3,767 operational taxonomic units (OTUs) were classified. In the two culture modes, the abundance and diversity of bacterial in the sediment were significantly higher than in the L. vannamei intestine under the monoculture mode, in the water and intestines of L. vannamei and T. ovatus under the mix-culture mode (P < 0.05). There was no significant difference between the intestinal flora structures of L. vannamei and T. ovatus in the monoculture mode (P > 0.05). The dominant phyla in the sediment under two culture modes were Proteobacteria, Bacteroidetes, and Chloroflexi. The microbial community structure in the water and L. vannamei intestine were similar in both culture modes. The dominant phyla included Cyanobacteria, Proteobacteria, and Actinobacteria, with their abundances ranging from 80.88% to 97.10%. Proteobacteria was the dominant phylum in each group of samples, and the dominant genus in both culture modes was GpIIa. There was little difference in microbial community structures under the two culture modes; while the culture mode did not affect the core phyla/genera, there were differences in relative abundance. The experimental results provide a reference for the exploration of efficient and specific probiotic screening and microbial formulation techniques.