The term “intestinal core microbiota” refers to the set of microbial taxa that consistently occur in a particular host in which microorganisms interact with each other in a contiguous environment . This would require to explore bacteria taxa abundance and occupancy across multiple samples that are often reduced to a unique sampling point at the end of a given trial, which risks to mismatch the succession of microbial communities over time. Besides, it is well documented that nutrition and feeding is a major factor driving the changes in gut microbiota composition and function of living organisms, including farmed fish. Considering together temporal and nutritional aspects, the aim of this study was to rethink in a dynamic manner the core microbiota composition of farmed gilthead seabream fed with standard or alternative feed formulations through the production cycle, coinciding with the extreme 2022-2023 climate period.
Juveniles of gilthead seabream (~15g) of Mediterranean origin (Avramar , Burriana , Spain) grew from May 2022 to February 2023 in a flow-through system (3000 L tanks) operated with natural photoperiod and temperature conditions at the IATS infrastructure under standard rearing conditions. During the trial, fish were fed with a CTRL fish meal-based diet , or alternative feeds with processed animal protein (PAP), or insect meal + bacterial protein (ALT) as a main fish meal replacer. At initial (May 2022, t0), intermediate (July 2022, t1; November 2022, t2) and final (February 2023, t3 ) sampling points, 12-16 animals per time and diet were sampled for adherent intestinal microbiota . Bacterial DNA was extracted, and V3-V4 region of 16S rRNA gene was sequenced with Illumina MiSeq platform and taxonomically assigned against SILVA v138.1 database. The core microbiota was defined for each time point by setting an occurrence threshold of more than 50% of individuals within each dietary group.
Partial Least Squares Discriminant Analysis (PLS-DA) disclosed 116 taxa (filtered by ≥0.1% abundance) of discriminant value (VIP>1), driving the cyclic trend of gut microbiota following changes in season . C ore microbiota analysis discerned always the consistent presence of 55, 58 and 83 taxa at t1, t 2 and t3 , respectively. The overlapping of these taxa generated a reduced list of 20 taxa, which were also represented at the beginning of the trial (t0). Overall, this constrained list represented >58% (45-72%) of the total intestinal microbiota regardless of sampling time and diet . Of note, 12 out of 20 core bacterial taxa exhibited a temporal discriminant role, while 8 persisted almost unaltered throughout the production cycle. Firmicutes and Actinobacteriota phyla are overrepresented in this bacteria fraction, becoming p robiotic candidate markers for promoting robust fish in a warming challenging scenario. Such approach was complemented with the construction of causal Bayesian networks to define gut microbiota associations, and their practical implications to stablish what is the most adequate probiotic solution for a given strain, physiological condition and rearing system.
This work was supported by MCIN with funding from European Union NextGenerationEU (PRTR-C17.I1) and by Generalitat Valenciana (THINKINAZUL/2021/024).