Fish microbiota research: Strengths and limitations for fast and low-cost profiling of intestinal gilthead sea bream (Sparus aurata) microbiota

Here, we aimed to examine the strengths and limitations of cost-effective methodologies for their use in aquaculture fish gut mucosal samples. Attention was focused on Oxford Nanopore Technology (ONT) MinION as a portable sequencing device that offers the possibility of a fast and low-cost bacteria profiling of intestinal mucus communities, using gilthead sea bream as a model of highly cultured farmed fish.