The immune response and microbial changes in the intestine of grass carp (Ctenopharyngodon idella) following GCRV-II infection.

Abstract

In vertebrates, survival during infection depends on the coordination between the host immune system and the gut microbiota. However, the crosstalk between gut microbiota and immune responses under pathogenic pressure remains poorly characterized in teleost fish. In this study, we performed transcriptomic and 16S rRNA sequencing to investigate the dynamic change of intestinal immunity and microbial communities following infection with grass carp reovirus genotype II (GCRV-II). Our analysis show that the foregut and midgut exhibited coordinated upregulation of innate immune genes, while the hindgut demonstrated a more pronounced and unique antiviral response. Notably, the hindgut also showed stronger activation of adaptive immunity during the recovery phase (28 DPI). Additionally, GCRV-II infection induced significant microbial dysbiosis, characterized by reduced diversity at 7 DPI and restoration of beneficial taxa (e.g., Bacillus) at 28 DPI. Correlation analyses further uncovered segment-specific microbiota-immune interactions, where pathobionts (e.g., Acinetobacter, Vibrio) positively correlated with immune activation, while commensals like Gemmobacter were associated with homeostasis. These results demonstrate a compartmentalized mucosal defense strategy in grass carp, wherein each intestinal segment plays distinct yet complementary roles in antiviral immunity and microbial regulation.