The interface between microbiota and the host mucosal functioning is a stage for numerous processes that are key for the host s´ defensive system. In aquaculture, opportunistic microorganisms are often harbored in mucosal systems, causing disease outbreaks when fish homeostasis is disrupted. The modulation of this interface by targeting undesirable bacteria is a strategy that has been tested through nutritional approaches, such as the inclusion of functional ingredients like prebiotics. In salmon aquaculture, mucosal health and well-functioning are among the most important topics, and the implementation of novel strategies is needed to support the welfare and boost the resistance of fish. In this study, we assess the modulation of the gut mucosa microbiota and its function in two different intestinal compartments ( proximal and middle intestine) by including the microalgae Euglena gracilis , with potential prebiotic effects in an ex vivo intestinal sac platform. The modulation of targeted microbial groups with opportunistic (e.g., Vibrio , Aeromonas , Tenacibaculum ) or beneficial (e.g., Lactobacillus , Bacillus) characteristics was screened through Nanopore MinION 16S long-read bacteriome sequencing and compared between the compartments’ mucosa exposed to an antibiotic treatment, or unexposed . An in-house bioinformatic pipeline was applied to retrieve the relative abundance of bacterial pathogens based on an aquaculture bacterial pathogen database with in-house modifications, and an in-house database of bacteria with reported beneficial impacts was used for comparison purposes . Moreover , the mucosa response was assessed and correlated with microbiota shifts following the transcriptional modulation of a panel of genes related to immune response, epithelium integrity, and homeostasis. Among all the identified potentially pathogenic bacteria, a group was affected by the exposure of the intestinal mucosa to microalgae, and some beneficial bacteria were also affected . The ratios Firmicutes:Bacteroidetes , and Proteobacteria:Bacteroidetes were modulated, increasing when mucosa was exposed to an antibiotic. This was evident in both compartments, and the opposite was observed when microalgae were included in the sac in one of the compartments. The expression of the acute inflammation markers indicated an impact on the mucosas´ health. Th rough the application of an ex vivo approach, it was possible to screen and highlight the impacts of a harmful compound and an algae-based functional ingredient.
Acknowledgments: This work was financially supported by the project MICROBOOST – PT-INNOVATION-0102 – funded by Iceland, Liechtenstein and Norway through the European Economic Area (EEA) grants