Consistent responses of the shrimp Litopenaeus vannamei gut microbiota to Enterocytozoon hepatopenaei infection across spatially distant farms

Abstract

The gut microbiota of aquatic animals is supposed to be sourced from rearing water. However, bacterioplankton communities exhibit a biogeographic pattern, raising the question whether the gut microbiota respond consistently to shrimp health status across spatially distant farms. Here, we collected shrimp Litopenaeus vannamei samples infected with Enterocytozoon hepatopenaei (EHP) from six geographically distant farms with varying local conditions. The gut microbiota of healthy shrimp differed significantly across aquaculture locations, while EHP infection effect was also detectable at each location. Therefore, we ruled out the location effect by removing taxa that featured location. After this optimization, we identified 23 EHP-discriminatory taxa that accurately diagnosed EHP infection, achieving an overall accuracy of 90.5%. Structural equation model revealed that water pH and NO3− levels were the governing factors for the bacterioplankton community. However, the shrimp gut microbiota was not strongly affected by the bacterioplankton community in their rearing water. EHP infection consistently increased deterministic processes and destabilized the biotic network in the shrimp gut microbiota. Collectively, our findings provide evidence that EHP infection causes consistent changes, e.g., altered structure, increased determinism, and destabilized network, in the gut microbiota across spatially distant farms. In particular, we established a diagnosis model for diagnosing EHP infection that is independent of aquaculture location.