Association of the microbiota dysbiosis in the hepatopancreas of farmed crayfish (Procambarus clarkii) with disease outbreaks

Abstract Symbiotic microorganisms in the hepatopancreas have been found in various crustaceans, and their vital role in maintaining host health has drawn increasing attention. However, the information about the symbiotic microbiota in the hepatopancreas of freshwater crayfish (Procambarus clarkii) is scarce. In this study, the high-throughput sequencing technology was used to characterize the bacterial communities in the hepatopancreas of P. clarkii at different health statuses, including healthy, anorexic, moribund, and whitish muscle statuses. Results showed that the hepatopancreatic microbiota of healthy crayfish was dominated by the phyla Firmicutes, Proteobacteria, and Bacteroidota and Clostridium sensu stricto 11, Proteus, C. sensu stricto 1, Paraclostridium, and Weissella. Distinct differences were found in the structure, composition, and predicted function of the hepatopancreatic microbiota between the healthy and the sick crayfish. The LEfSe analysis revealed that the symbiotic bacterial species, including Proteus penneri, C. sensu stricto 11 and Lactococcus garvieae, and the potential probiotics, such as Weissella cibaria and Lactobacillus murinus, in the hepatopancreas of healthy crayfish were significantly enriched than those of sick crayfish, whereas the opportunistic pathogens, including Citrobacter freundii, Plesiomonas shigelloides, C. sensu stricto 7, and Terrisporobacter, in the hepatopancreas of sick crayfish were significantly enriched than those of healthy crayfish. In addition, compared with that of healthy crayfish, the hepatopancreas of moribund crayfish had significantly enriched bacterial genera, such as Dubosiella, Candidatus, Bacilloplasma, and Phreatobacter, whereas the hepatopancreas of crayfish with whitish muscle disease was observed with a significant enrichment of some opportunistic pathogens, including Morganella morganii, Providencia alcalifaciens, Vagococcus fluvialis, Clostridium lundense, and Bacteroides. This apparent dysbiosis, which showed the increase in opportunistic pathogens and the decrease in symbiotic microorganisms (including potential probiotics), might represent a specific microbial signature of disease occurrence. Furthermore, the PICRUSt2 analysis revealed that the microbial functions involved in carbohydrate metabolism and xenobiotic biodegradation in the hepatopancreas of sick crayfish were significantly enriched than those of healthy crayfish, whereas the microbial functions involved in amino acid metabolism, lipid biosynthesis, biosynthesis of other secondary metabolites, energy metabolism, nucleotide metabolism, transport and catabolism, and immune system in the hepatopancreas of healthy crayfish were significantly enriched compared with those of sick crayfish. This study revealed the hepatopancreatic microbiota dysbiosis associated with disease outbreaks, providing potential indicators for assessing the health status of crayfish and new clues for exploring the potential role of the hepatopancreatic microorganisms in affecting host health and disease.