Vibrio parahaemolyticus infection in Manila clams (Ruditapes philippinarum): A case study of microbiome perturbation

The homeostasis of gill microbiota is essential for marine organisms' health, yet pathogen invasion disrupt this balance, impacting host physiology. As the farming density rises in the shellfish aquaculture industry, the Manila clam (Ruditapes philippinarum) has shown increased susceptibility to pathogens, with Vibrio parahaemolyticus representing a major economic threat. This study delves into the effects of V. parahaemolyticus on the gill microbiota of R. philippinarum (Ruditapes philippinarum) through histopathological analysis and 16S rRNA gene sequencing. At 72 hour post-infection (hpi), severe inflammatory reactions and gill damage were observed, accompanied by significant changes in microbial community structure. At 72 hpi, microbial diversity significantly shifted, with a decrease in Bacteroidota and Vibrionimonas, while Bradyrhizobium became dominant. By 96 hpi, Acidobacteriota and Chloroflexi increased, suggesting organic matter accumulation and redox alterations. LEfSe analysis identified Enterobacteriaceae, Streptomycetaceae, and Streptomycetales as biomarker taxa at 72 hpi. Metabolic pathways with increased abundance relative to 0 hpi included nucleoside metabolism, replication, and purine metabolism, while glycine, serine, and threonine metabolism showed a decreased abundance. Our findings illustrate that V. parahaemolyticus infection disrupts microbial and metabolic homeostasis in the gill of R. philippinarum, eliciting substantial inflammatory damage and offering insights into molecular mechanisms underlying clam susceptibility and potential mortality.