The microsporidian Enterocytozoon hepatopenaei (EHP) is an emerging pathogen that causes substantial economic losses in shrimp (Penaeus spp.) aquaculture worldwide. To prevent diseases in shrimp, the manipulation of the gut microbiota has been suggested. However, prior knowledge of the host-microbiome is necessary. We assessed the modulation of the microbiome (bacteria/fungi) and its predicted functions over the course of disease progression in shrimp experimentally challenged with EHP for 30 days using high throughput 16S rRNA and ITS amplicon sequencing. Infection grade was assessed for the first time by quantitative digital histopathology. According to the infection intensity, three disease-stages (early/developmental/late) were registered. During the early-stage, EHP was not consistently detected, and a high diversity of potentially beneficial microorganisms related to nutrient assimilation were found. In the development-stage, most of the shrimp start to register a high infection intensity related to a decrease in beneficial microorganisms and an increase in opportunistic/pathogenic fungi. During late-stage, animals displayed different infection intensities, showed a displacement of beneficial microorganisms by opportunistic/pathogenic bacteria and fungi related to pathogen infection processes and depletion of energetic reserves. The degenerative cyclic pattern of EHP infection and its effects on beneficial microorganisms and beneficial functions of the shrimp hepatopancreas microbiome are discussed.
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