Deep insight into bacterial community characterization and relationship in the pond water, sediment and the gut of shrimp (Penaeus japonicus)

This study characterizes the composition, diversity, function and interspecies interaction of the bacteria community in the gut of shrimp (Penaeus japonicus) and its culture water and sediment by 16S rRNA gene high-throughput sequencing. The relationships of bacterial communities in the gut and the surrounding water and pond sediment were compared and quantified. The sediment bacteria exhibited the highest α-diversity. The bacterial communities were distinctly clustered according to the habitats. Different habitats exhibited a low (8% ~14.12%) similarity of the bacteria community in taxonomic composition, but a surprisingly high (88.77% ~ 92.57%) similarity in functional composition. The proportion of negative links were more abundant in the sediment bacterial networks (51%) than those in the gut and water bacterial networks (8% and 2%, respectively). SIMPER analysis revealed that the bacterial community in the gut was more similar to the sediment than to the water. SourceTracker analysis showed that the sediment is a more important source of the bacterial contributor (64.58%) to the shrimp gut than the pond water (35.32%). Our results have important implications for establishing sustainable microbial management strategies for shrimp farming and also provide information to understand the environmental mechanism of gut bacterial community assembly. •Different habitats exhibited a low similarity of bacteria community, but a high similarity in functional composition.•Negative interactions were more abundant in the sediment bacterial networks than those in the gut and water networks.•Sediment contributed greatest to the source of shrimp gut and water bacteria.