Gut microbiota dynamics in carnivorous European seabass (Dicentrarchus labrax) fed plant-based diets

Abstract

A healthy gastrointestinal microbiota is essential for host fitness, and strongly modulated by host diet. In aquaculture, a current challenge is to feed carnivorous fish with plant-feedstuffs in substitution of fish meal, an unsustainable commodity. Plants have a limited nutritive value due to the presence of non-starch polysaccharides (NSP) which are not metabolized by fish. In this work we assessed the effects of NSP-enriched diets on European seabass gut microbiota and evaluate the selective pressure of plant feedstuffs towards gut microbes with NSP-hydrolytic potential, i.e. capable to convert indigestible dietary constituents in fish metabolites. Triplicate groups of European seabass juveniles were fed a fish meal-based diet (control) or three plant-based diets (SBM, soybean meal; RSM, rapeseed meal; SFM, sunflower meal) for 6 weeks, before recovering intestinal samples for microbiota analysis, using the Illumina’s MiSeq platform. Plant-based diets impacted differently digesta and mucosal microbiota. A decrease (p = 0.020) on species richness, accompanied by a decline on the relative abundance of specific phyla such as Acidobacteria (p = 0.030), was observed in digesta samples of SBM and RSM experimental fish, but no effects were seen in mucosa-associated microbiota. Plant-based diets favored the Firmicutes (p = 0.01), in particular the Bacillaceae (p = 0.017) and Clostridiaceae (p = 0.007), two bacterial families known to harbor carbohydrate active enzymes and thus putatively more prone to grow in high NSP environments. Overall, bacterial gut communities of European seabass respond to plant-feedstuffs with adjustments in the presence of transient microorganisms (allochthonous) with carbohydrolytic potential, while maintaining a balanced core (autochthonous) microbiota.

Black soldier fly meal effects on meagre health condition: gut morphology, gut microbiota and humoral immune response

“…The bacteria genera identified in meagre autochthonous population were similar to that found in other carnivorous fish gut, including European seabass (Nikouli et al, 2018;Serra et al, 2021), gilthead seabream (Nikouli et al, 2018), Atlantic salmon (Gajardo et al, 2016;Villasante et al, 2019), or rainbow trout (Rimoldi et al, 2018). Bacteria belonging to Pseudomonas and Burkholderia genera, which include pathogenic species but also potential probiotic strains, are abundant in aquatic environments and were previously found at high levels in European seabass, gilthead seabream, Atlantic salmon, and rainbow trout gut (Gajardo et al, 2016;Nikouli et al, 2018;Rimoldi et al, 2018;Serra et al, 2021). Bacillus spp., mostly associated with beneficial characteristics, were also reported to be highly prevalent in the gut of European seabass, gilthead seabream, white seabream (Diplodus sargus) (Santos et al, 2021;Serra et al, 2019), Atlantic salmon (Gajardo et al, 2016;Villasante et al, 2019), and rainbow trout (Rimoldi et al, 2018).…”

“…Gut microbiota composition was assessed in pooled samples of 2 fish per tank to reduce variability (n=3). Bacterial genomic DNA was extracted from 300 mg of digesta and mucosa, following the procedure described in Serra et al (2021). Bacterial 16S rRNA gene fragments were amplified by a touchdown PCR on a T100™ Thermal Cycler (Bio-Rad Laboratories Lda., Amadora, Portugal), using oligonucleotide primers 16S-358F (which has a GC clamp at the 5´end) and 16S-517R (Muyzer et al, 1993).…”

Effect on Intermediary Metabolism and Digestive Parameters of the High Substitution of Fishmeal with Insect Meal in Sparus aurata Feed

“…Transient species, mostly associated with external environmental and nutritional factors, are thought to play some significant roles depending on their colonization ability [71]. Thus, species able to survive the conditions in the gut and adhere to intestinal mucosa may become permanent residents [72] and perform primary functionality [73]. The result described in this paper showing the grouping of T50 and C samples, and leaving treatment most microbiologically similar to C, H50M, out of this group, may be explained by this theory.…”

Robust host source tracking building on the divergent and non-stochastic assembly of gut microbiome in wild and farmed large yellow croaker

“…[75][76][77][78]. In carnivorous European seabass, mucosa-associated microbiota was found more stable than the corresponding digesta microbiota when shifting to a plant-based diet [77].…”

“…The rapid shift (from days to few months) of gut microbiota during domesticated and diet change have been revealed in African cichlid, European seabass, grass carp, perch, etc. [75][76][77][78]. In carnivorous European seabass, mucosa-associated microbiota was found more stable than the corresponding digesta microbiota when shifting to a plant-based diet [77].…”