High throughput sequencing of microbial communities associated with farmed Genypterus chilensis reveals the presence of uncultured pathogens. Microbial community associated to G. chilensis

Red conger eel (Genypterus chilensis, Guichenot) is a native Chilean species whose meat is characterized by high gastronomic demand and is now part of the Chilean aquaculture diversification program. Two disease outbreaks derived from its intensified aquaculture farming have been reported and were associated with Vibrio spp. and Tenacibaculum spp. However, the role of individual species is not clear because there is a lack of information about the bacterial community composition associated with healthy specimens of this fish species. Therefore, additional studies to determine the composition of the autochthonous microbiota and their antimicrobial susceptibilities are warranted in order to improve the success of red conger eel farming. In this study, we described the bacterial community associated with G. chilensis by culturing methods and high throughput sequencing. By culturing, the predominant genera were Vibrio, Pseudolteromonas; Aliivibrio; Shewanella. Psychromonas. Only a few isolates showed amylase, gelatinase or lypase activity and almost all isolates showed inhibition zones to most common antibiotics used in aquaculture. Nevertheless, by high throughput sequencing the predominant genera were Paperlucidibaca, Colwellia, Polaribacter Saproespiraceae and Tenacibaculum, while Vibrio represented only the 27th most abundant genus. Moreover, using this approach we could link an increase in the relative abundance of Vibrio and Tenacibaculum to previous outbreaks that occurred in the facility. Therefore, monitoring the presence and abundance of these potential pathogens could be useful in providing prophylactic measures to prevent future outbreaks.