Intestinal microbial profiling of grass carp (Ctenopharyngodon idellus) challenged with Aeromonas hydrophila

Abstract Bacterial enteritis caused by Aeromonas hydrophila is one of the most common diseases in grass carp culture. There have been intensive reports on grass carp after A. hydrophila infection at the molecular level, but analyses of the intestinal microbiota are rare. In this study, histopathological sections were examined, and 16S rRNA sequencing was used to study the changes in the intestinal tissue and microbiota of grass carp after infection with A. hydrophila. Histological analysis indicated that the symptoms appeared at 12 h, were most severe at 6 d and 9 d, and did not recover until 15 d. Based on the community structure and diversity of the intestinal microbiota, acute fluctuations and dramatic increases occurred at 12 h, with decreases at 24–72 h, a rapid increase at 6–9 d and subsequent somewhat recovery. Four phyla (Proteobacteria, Fusobacteria, Bacteroidetes and Firmicutes), especially Proteobacteria, reflected fluctuations in the intestinal microbial composition at different time points. Potential functions also showed that immune- or disease-related pathways might dominate as feedback responses to pathogen (A. hydrophila) stimulation, and the expression of most of the marker functions increased from 0 h to 12 h, decreased at 24 h–72 h, increased to a peak at 6 d or 9 d, and then again decreased at 15 d. These findings could elucidate the dynamic changes in the intestinal microbiota that occur in response to A. hydrophila infection and might shed light on the mechanism of fish intestinal pathogenesis from the perspective of the intestinal microbiota.