A novel fish meal-free diet formulation supports proper growth and does not impair intestinal parasite susceptibility in gilthead sea bream (Sparus aurata) with a reshape of gut microbiota and tissue-specific gene expression patterns

Genetics and Nutrition Drive the Gut Microbiota Succession and Host-Transcriptome Interactions through the Gilthead Sea Bream (Sparus aurata) Production Cycle

“…We also observed a decrease in the expression of the pro-inflammatory il8 and cxcl9 genes in GS-FUTURE fish in comparison to the REF-FUTURE group, concurrent with the increase in Bacilli-related taxa (Bacilli and Gemella ). Previous studies in gilthead sea bream using qPCR-arrays have already stated this association [ 17 , 18 ], and the current analysis reinforces the anti-inflammatory and anti-oxidant properties of this taxonomic class [ 122 ], commonly used as a probiotic to improve the growth and gut health of livestock fish [ 123 , 124 ]. Lastly, a total of 10 transcripts of the principal protein components of the ECM ( anxa2 , chrm2 , col18a1 , lama2 , itga6 , myh10 , postn , ptk2b , selp and stab1 ) [ 125 ] were up-regulated in GS-FUTURE fish in comparison to GS-CTRL, suggesting an enhanced remodeling of the extracellular architecture.…”

“…Otherwise, as seen before for PROGENSA ® selected fish [ 23 ], the genus Clostridium was also increased in the GS fish (∆6% along the trial). The Clostridiales order is a known promoter of the production of short-chain fatty acids (SCFAs), related to anti-inflammatory properties and disease resistance [ 18 , 79 ]. Therefore, it is tempting to consider the abundance of this taxa as a suitable indicator of the impact of gilthead sea bream selection programs on gut health, regardless of seasonality and developmental stage.…”

“…Like in other animals, the gut microbiome of fish contains thousands of microbial species that establish a complex network of relationships among each other and with the host [ 14 , 15 , 16 ]. Indeed, both the transient and resident gut microbial communities produce a number of metabolites that impact the host functions not only at the local level, but also at a distant one [ 17 , 18 ]. As part of this complex puzzle, the modulatory effect of the diet on the intestinal microbiota has been extensively documented in some farmed fish, including gilthead sea bream ( Sparus aurata ) [ 2 , 19 ] and European sea bass ( Dicentrarchus labrax ) [ 20 , 21 , 22 ].…”

“…However, recent studies in gilthead sea bream pointed out that intensive selection for fast-growth co-selects for a plastic gut microbiota with a wider metabolic response to cope with changes in diet composition [ 23 , 24 ]. Links between gut microbiota and the host-transcriptome have also been established in gilthead sea bream, using targeted [ 17 , 18 , 22 ] or massive gene expression [ 25 ] approaches. However, most of this research is focused on stationary models in a given geographical location, and further research is needed to establish the temporal trends for most of the host-associated bacterial successions with changes in age, sex, season, nutrition and rearing conditions [ 26 , 27 , 28 ].…”

SAMBA: Structure-Learning of Aquaculture Microbiomes using a Bayesian Approach

“…Thus, there is only technical variability within replicates, allowing elucidation of the relationships and their associated taxa predicted values (Supplementary Data File, Section Case-Study Validation). Second, we used a pan-microbiome dataset derived from three feeding trials with the same starting point (May 2020) and location (40°5 ′ N; 0°10 ′ E) and including sibling fish purchased at the same Mediterranean hatchery (Piscimar, Burriana, Spain) (Naya-Català et al, 2021; Solé-Jiménez et al, 2021; Piazzon et al, 2022). These three datasets derive from the real-world observation and were thus important to test how SAMBA manages the technical and/or biological variability among microbiomes of distinct specimens.…”