Monitoring Fish Bacterial Pathogens of Wild Fish Species From the South China Sea by Applying Next‐Generation Sequencing on Gill Tissue

The classic epidemiological triangle model of host-environment-pathogen is recently being reshaped into a tetrahedron, with the growing understanding of the importance of the microbiome in this array. The gills, being a gateway into the fish body, bearing an important role in fish homeostasis, host a complex microbiome that reflects the ambient water, while also showing resemblance to gut microbiome. Next-generation sequencing (NGS) and improvements in data analysis tools enable researchers to gather and analyse a lot more data than ever before, take a closer, more detailed look at microbiota, and gain a much better understanding of the biological processes at work in these complex relations. Here, 16S rRNA amplicons of bacterial DNA extracted from the gills of 36 asymptomatic specimens of three wild fish species from the South China Sea (Nemipterus japonicus, Alepes djebaba, and Saurida tumbil) were sequenced using NGS. Data analyses revealed the presence of 20 potentially pathogenic species, including several zoonotic agents. Gill microbiota exhibited host species-specificity, and expressed a significant difference between demersal and pelagic-amphidromous fish. It is suggested that this method be more widely implemented, in order to gain more insight on ocean ecosystems' health status, as well as fish stocks of commercial importance.