One of the aims of AQUAEXCEL3.0 WP4 (Technological Tools for Improved Experimental Procedures) is the establishment and validation of the use of Nanopore technologies for a standard protocol of real-time monitoring of microbial communities in water and fish samples (gut and skin mucosa, faeces) at experimental infrastructures. Major advances have been conducted towards this goal, and this protocol constitutes at present one of the main points of the offer of the analytical platform of CSIC at Institute of Aquaculture Torre de la Sal (IATS-ANA).
Initially, PCR conditions of the 16S rRNA MinION protocol for gut microbiotal profiling were optimized (Toxqui-Rodríguez et al, 2023. Aquaculture 569, 739388). More recently, Nanopore sequencing downstream methodologies such as library preparation strategies, primers, or basecalling models have also been standarized to conduct a fast and reproducible protocol to be used as a reference for fish-associated samples. This optimized protocol will be shortly submitted to International Journal of Molecular Sciences (Domingo-Bretón et al., 2024).
As a proof of the successful and reproducible use, up to four AQUAEXCEL3.0 Transnational Accesses (TNAs) are taking advantage of Nanopore technology at CSIC IATS-ANA infrastructures, covering different topics of interest for three important farmed fish (gilthead sea bream, European sea bass and tilapia) studying the impact of different stimulus, such as the culture system, diets and feed additives on the microbiota modulation.
CIIMAR (Portugal) PhD student Ricardo Matias visited CSIC infrastructures for the conduction of a feeding trial (RAYON2BASS) assessing the impact of cellulose microfibers-based diets on the growth of European sea bass, followed by a multi-tissue transcriptome and water, gut and skin microbiota.
PhD student Eliza Syropoulou, from Wageningen University (The Netherlands) evaluated in BREAMUCOSA TNA the combined impact of culture system (open flowthrough or different degrees of water renewal in closed systems) and carbohydrate sources in gilthead sea bream diets on the microbiome composition of water, biofilms and skin and gut mucoses, and how microbiome changes affect fish growth and performance.
CCMAR (Portugal) PhD student Ibón García-Gallego analyzed within the FISH+ (Enhanching Fish Robustness Through Dietary Functional Additives) TNA the gut microbiota communities of samples from gilthead sea bream juveniles fed diets enriched with selected additives (thymol, butyrate, taurine), in order to assess the impact of such additives on the enhancement of intestinal health of cultured fish.
Finally, two researchers from University of Sabana (Colombia) will visit shortly IATS-ANA infrastructure within TILAPIAMICRORAS TNA, which seeks to assess the microbial ecology of healthy fingerlings, juveniles, and adult tilapia within recirculating aquaculture systems (RAS) and aquaponics systems in Colombia. The goal to reinforce the use of Nanopore MinION as a portable sequencing tool to study the skin and gut microbiomes of fish, which could significantly facilitate the integration of high-tech solutions in remote areas.
