Transcriptomic and Metagenomic Analyses of Snout Otter Clams (Lutraria rhynchaena) Infected with Swollen-Siphon Disease
Swollen-siphon disease has caused significant mortality in snout otter clams (Lutraria rhynchaena), a valuable aquaculture species in Vietnam, yet its causative agent remains unidentified. In this study, integrated transcriptomic and metagenomic data were analyzed to investigate host molecular responses to the disease and to further re-evaluate its microbial basis. The authors conducted a controlled disease-challenge experiment, demonstrating the presence of a transmissible pathogenic agent and a significantly higher mortality rate in the experiment group, up to 100% by day 6 postinjection. Transcriptomic profiling of siphon and body tissues from diseased (n = 4) and healthy clams (n = 4) identified 508 differentially expressed genes (DEG), including 308 upregulated and 200 downregulated in diseased samples. Upregulated DEG such as cd109, chit1, and duox2 indicate enhanced innate immune responses against microbial pathogens, whereas downregulated genes, including hsp70, hsc70, and hsp68, suggest suppressed stress responses. Gene ontology enrichment revealed activation of immune signaling and suppression of energy metabolism and muscle contraction. The analysis of metagenomic data identified viral communities dominated by Heunggongvirae, Monodnaviria, and unclassified viruses. Although potential pathogenic taxa were detected, their role in disease etiology needs to be further investigated. The transcriptomic profiling presented in this study provides insights into host–pathogen interactions underlying swollen-siphon disease in snout otter clams, supporting future studies on disease etiology and epidemic control.