Longitudinal analysis of changes in the gut microbiota of zebrafish following acute spring viremia of carp virus infection

Abstract

The gut microbiota of vertebrates plays a critical role in resistance to invading pathogens. Spring viremia of carp (SVC) is one of the most severe viral diseases in aquaculture. The causative agent is the SVC virus (SVCV), resulting in devastating damage to cyprinid. Yet, knowledge regarding the relationship between the gut microbes and disease is still lacking, particularly the dynamic alteration of the gut microbiota in fish following SVCV infection. To understand the longitudinal effects of SVCV infection on the microbiota of the zebrafish intestine, an intraperitoneal injection zebrafish model mimicking acute SVCV infection in fish with typical virologic and pathologic features was used. Intestinal microbes from both control (CON) and SVCV-infected fish were characterized at various time points by 16S ribosomal RNA gene V3-V4 region sequencing. Viral load in spleen, kidney, and intestine and the total bacterial load in the gut were detected by qPCR.The results showed that SVCV infection was associated with alterations of the gut microbiota in zebrafish as indicated by both alpha and beta diversity indexes. Compared with the CON group, SVCV-infected fish had significantly reduced bacterial diversity at 4 to 6 days post-infection (dpi). It has been found that a number of bacteria were enriched in opportunistic pathogens and depleted of beneficial commensals, at the time of onset of obvious symptoms or even death and at the time of complete disappearance of symptoms. A noticeably higher relative abundance of opportunistic pathogens, such as Clostridium_XlVa, Vibrio, Aeromonas, Mycoplasmataceae_unclassified, and Rothia; and a lower relative abundance of beneficial symbionts were found in the gut microbiome at 4, 7, 10 days post-infection. Five biomarkers showed high accuracy for distinguishing SVCV-infected fish from CON with an area under the curve (AUC) up to 0.78, 0.80, 0.79, 0.89, and 0.84, respectively. The relative abundance of Enterobacteriaceae_unclassified showed a positive correlation with viral loads of SVCV and the relative abundance of Cetobacterium and Aeromonas were positively related to the bacterial load in the gut, while the same results were observed for the corresponding two phyla (Fusobacteria and Proteobacteria). SVCV causes long-term gut microbiome dysbiosis, which is linked to viral load in target organs and total intestinal bacterial count. The results of our study suggest the potential value of the gut microbiota as a diagnostic biomarker and therapeutic target for SVC, but further validation is required.