Gut microbiota modulation and immunity response induced by Citrobacter freundii strain GC01 in grass carp (Ctenopharyngodon idellus)

Abstract The effect of Citrobacter freundii, an opportunistic pathogen of fish, on the gut microbiota and immune responses in fish remains unknown. We fed grass carp (Ctenopharyngodon idellus) with two different concentrations of this bacterium (experimental Low and High groups, plus Control group). No signs of acute inflammatory response were found in either of the experimental groups using the intestinal HE staining method, but the number of intestinal goblet cells was much higher in the High group. Furthermore, we found that feeding C. freundii significantly decreased the alpha diversity and altered beta diversity of gut microbiota in both groups, and significantly promoted the relative abundance of Enterobacteriales, Pasteurellales, Neisseriales and Citrobacter in the High group. Spleen transcriptome showed that the expression pattern of immune system-related genes varied significantly between the Control group and High group. Several immunity-related pathways and two infectious diseases-related pathways were significantly enriched in the High group. Many complement system genes, including c3, c4, c5, c7, c8a, c8b and c1s, were also up-regulated in the High group. Overall, our results indicate that C. freundii did not trigger acute intestinal inflammation, but it changed the diversity and population structure of gut microbiota, and triggered the host's innate mucosal immune system. The enrichment of two infectious diseases-related pathways also suggested a higher risk of infection in the High group. These results contribute to our understanding of the effects of opportunistic fish pathogens on gut microbiota and host's immune responses.