Quantifying dominant bacterial genera detected in fish eggs and larvae metagenomic 16S rRNA gene data using genus-specific primers

The goal of this study was to design genus-specific primers for rapid evaluation of the most abundant bacterial genera identified using amplicon-based sequencing of the 16S rRNA gene in fish-related samples and surrounding water. Efficient genus-specific primers were designed for eleven bacterial genera including Alkalimarinus, Colwellia, Enterovibrio, Marinomonas, Massilia, Oleispira, Phaeobacter, Photobacterium, Polarbacerium, Pseudomonas and Psychrobium. The alignment and identity of 16S rRNA genes and genus-specific primer sequences of different bacterial species of each target bacterial genus are specified. The forward (in green) and reverse (in pink) primers (5ʹ to 3ʹ) highlighted at the top of the alignment are specific for each bacterial genus. The name of species that their 16S rRNA genes are not 100% identical to the primers and may not be amplified with the primers are colored with yellow.