Differentially Expressed Infection-Associated Genes in a Shewanella algae isolate From a Deceased Northern Bottlenose Whale

Diseases are an important but poorly understood influence on marine ecosystems. However, many pathogens of wild marine organisms remain poorly characterized, limiting our understanding of their ecology and potential impacts. This study investigates the potential virulence mechanisms of a Shewanella algae strain isolated from the brain tissue of a deceased northern bottlenose whale (Hyperoodon ampullatus). Using long-read Oxford Nanopore RNA Sequencing, differential gene expression analysis (DGEA) was conducted comparing growth in standard media, Tryptic Soy Broth (TSB) and TSB supplemented with 5% brain homogenate (BH) to stimulate expression of genes potentially associated with virulence. Twenty-eight significantly differentially expressed genes (23 identified using the assembled genome and five additional non-overlapping genes detected using a closely related reference genome) were identified out of 7,213 genes with at least two primary mapped reads. These genes were associated with processes that have been linked to bacterial virulence in previous studies, including protein translocation (e.g., small signal recognition particle), flagellar motility, chemotaxis, and iron acquisition. Functional analysis indicated an increased expression of pathways related to amino acid metabolism and motility, whereas carbohydrate and inorganic ion transport were downregulated. These results suggest that environmental cues, potentially including factors related to iron metabolism, may influence bacterial virulence, obtained using Oxford Nanopore RNA sequencing for pathogen transcriptomics.