Background: Enterocytozoon hepatopenaei (EHP), infects P.vannamei and causes hepatopancreatic microsporidiasis associated with severe growth retardation in shrimp culture. The influence of EHP in the shrimp gut microbiota is poorly studied&nbsp;and this would be an interesting area to investigate. In this study, metagenomic approach was followed to compare the overall species richness of the gut microbiota in healthy and EHP-infected P. vannamei. 
 
Methods: Bacterial genomic DNA from gut samples of EHP-infected and healthy shrimps were profiled for the 16S rRNA gene, targeting the V3-V4 conserved region. Operational Taxonomic Units (OTUs), were identified and clustered together with a cutoff of 97% identity using UCLUST. The OTUs were then used for the computation of alpha diversity and beta diversity for each sample. 
 
Result: Gut samples from EHP-infected shrimp showed lower bacterial abundance throughout the family, class, order, and genus levels. This research also highlights that EHP not only affects the hepatopancreas of the shrimp, but it also has the ability to affect the shrimp gut, predisposing them to other opportunistic infections.

Metagenomic Study on the Influence of Enterocytozoon hepatopenaei (EHP) Infection on the Gut Microbiota in Penaeus vannamei

Background: Enterocytozoon hepatopenaei (EHP) is a microsporidian parasite that infects Pacific white shrimp (Penaeus vannamei). EHP infection causes severe growth retardation and subsequent economic losses, thereby posing a major challenge in shrimp farming. Understanding the diversity of microbiota in EHP-infected shrimp hepatopancreas (HP) is essential, as the organ plays a crucial role in nutrient storage, absorption and growth.&nbsp; 
 
Methods: A metagenomic approach was employed, targeting the V3-V4 conserved region of the 16S rRNA gene to gain insights into the microbiome dynamics of P. vannamei HP in response to EHP infection. Operational Taxonomic Units (OTUs) were identified from the sample reads using sequence similarity based on the 16S bacterial reference database (Greengenes) and the OTUs were clustered together using UCLUST at a cut-off of 97% identity.&nbsp; 
 
Result: The analysis revealed a varied OTU abundance between healthy and EHP-infected HP samples. Higher levels of pathogenic Vibrionales, Pseudoalteromonadaceae, Vibrio and Photobacterium damselae were found in EHP-infected HP samples, linked to Acute Hepatopancreatic Necrosis Disease (AHPND) and White Feces Syndrome (WFS) in shrimp, suggesting a possible pathobiome interaction in conjugation with EHP. Furthermore, specific taxa like Sphingomonadaceae, Chitinophagaceae, Cytophagaceae, Verrucomicrobiaceae, Xanthomonadaceae, Pseudomonas and Kaistobacter were more abundant in healthy P. vannamei HP, suggesting their potential as health biomarkers to assess the overall health status of the shrimp.

Metagenomic Profiling Identifies Potential Biomarkers for Shrimp Health Assessment and Pathobiome-like Association Involving WFS/AHPND Associated Bacteria in Enterocytozoon hepatopenaei (EHP)-infected Penaeus vannamei