Two strategies to unravel gene expression responses of host-microbe interactions in cod (Gadus morhua) larvae

Abstract

The commensal bacteria in the intestine play essential roles in the development and functionality of the host. To unravel the host–microbe interactions in Atlantic cod (Gadus morhua L.) larvae, we used two molecular approaches: (1) suppression subtractive hybridization-polymerase chain reaction (SSH-PCR) to identify host gene responses and (2) expression analysis of selected genes reported to be differentially expressed in gnotobiotic zebrafish in a previous study to determine whether these host responses are also conserved in cod. Suppression subtractive hybridization-PCR identified 156 transcripts putatively regulated by the presence of bacteria. However, out of 22 selected transcripts, only four were significantly differentially expressed when quantified using quantitative (real-time) PCR. Expression analysis of selected genes from zebrafish revealed possible conservation of host responses for three out of eight genes analysed. For most of the genes quantified, the gene expression pattern varied between two biological replicates. This may reflect differences in the bacterial composition in the rearing bottles, and denaturing gradient gel electrophoresis analysis confirmed significant differences between the two replicates with regard to bacterial diversity. The varying effects on gene expression caused by differences in the microbial composition show the necessity of further studies where axenic cod larvae are compared with larvae raised in defined and controlled (gnotobiotic) environments.