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

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.

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.

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.