In silico detection of a candidate disease-associated microorganism in metagenomic data from otter clams (Lutraria rhynchaena Reeve, 1854) affected by swollen siphon disease

Swollen siphon disease causes substantial mortality and economic losses in farmed snout otter clams (Lutraria rhynchaena) in Vietnam, yet its causative agent remains unknown. In this study, we performed metagenomic assembly and reconstructed metagenome-assembled genomes (MAGs) from available shotgun sequencing data of diseased siphon tissues. Assembly with metaSPAdes, viral identification with the geNomad pipeline, and genome binning with SemiBin yielded 219,737 contigs and four MAGs. Taxonomic profiling of assembled contigs revealed a bacteria-dominated metagenome (77%), primarily composed of Pseudomonadota, and an order-of-magnitude more annotations than previously reported. Caudoviricetes (~90%), a class of tailed bacteriophages, overwhelmingly dominated the viral contigs suggesting involvement of bacterial hosts associated with Caudoviricetes such as Vibrio spp., in disease etiology. Among the recovered MAGs, only one quality-sufficient MAG (bin 3; completeness 65.21%) was obtained and taxonomically assigned to the family Simkaniaceae (order Chlamydiales). Despite its partial genomic recovery, bin_3 encoded a near-complete type III secretion system and other intracellular lifestyle-associated features, including 247 putative virulence-associated genes. Our findings identify the Simkaniaceae-related bacterium as a candidate disease-associated microorganism. We hypothesize that it may compromise host immunity and facilitate opportunistic Vibrio infection, although this association is correlative and remains to be evaluated. Future experimental validation is needed to assess causality and inform disease prevention strategies