This study investigated the profile of the autochthonous gut bacterial communities in adult individuals of Sparus aurata and Dicentrarchus labrax reared in sea cages in five distantly located aquaculture farms in Greece and determine the impact of geographic location on them in order to detect the core gut microbiota of these commercially important fish species. Data analyses resulted in no significant geographic impact in the gut microbial communities within the two host species, while strong similarities between them were also present. Our survey revealed the existence of a core gut microbiota within and between the two host species independent of diet and geographic location consisting of the Delftia, Pseudomonas, Pelomonas, Propionibacterium, and Atopostipes genera.

This study investigated the impact of different dietary ingredients, with different protein/lipid sources, on midgut and faeces bacteria community structures just before feeding and 3 h after feeding a single meal to individual rainbow trout (Oncorhynchus mykiss). Fish were kept in experimental rearing facilities and fed ad libitum twice daily for 5 weeks. Fish were fed three different commercial diets, which contained variations of high or low marine fishmeal/fish oil content. DNA was extracted from midgut and faeces samples for analysis of their bacterial 16S rRNA gene diversity by targeting the V3-V4 region with 454 pyrosequencing. A total of 332 unique bacterial operational taxonomic units (OTUs) were revealed in all samples. However, each sample was dominated (>80% relative abundance) by 2–14 OTUs, with the single most dominant OTU having >30% dominance, indicating that only a few bacteria were fundamental in terms of relative abundance in each treatment. Fifteen OTUs occurred in all samples (core microbiota). The majority of these OTUs belonged to the Proteobacteria, Firmicutes or Tenericutes, and were associated with other animal gut environments. The faecal material and the midgut samples had few overlaps in their shared OTUs. A postprandial response in the gut bacterial community structure 3 h after feeding highlights how dietary stimulation induces structural changes in the microbiota profiles in the established gut bacteria. This study showed that feeding O. mykiss different diets and even single meals lead to perturbations in the established gut bacteria of O. mykiss.

One of the most widely reared fish in the Mediterranean Sea is Sparus aurata. The succession of S. aurata whole-body microbiota in fertilized eggs, five, 15, 21 and 71 days post hatch (dph) larvae and the contribution of the rearing water and the provided feed (rotifers, Artemia sp. and commercial diet) to the host’s microbiota was investigated by 454 pyrosequencing of the 16S rRNA gene diversity. In total, 1917 bacterial operational taxonomic units (OTUs) were found in all samples. On average, between 93 ± 2.1 and 366 ± 9.2 bacterial OTUs per sample were found, with most of them belonging to Proteobacteria and Bacteroidetes. Ten OTUs were shared between all S. aurata stages and were also detected in the rearing water or diet. The highest OTU richness occurred at the egg stage and the lowest at the yolk sac stage (5 dph). The rearing water and diet microbial communities contributed in S. aurata microbiota without overlaps in their microbial composition and structure. The commercial diet showed higher contribution to the S. aurata microbiota than the rearing water. After stage D71 the observed microbiota showed similarities with that of adult S. aurata as indicated by the increased number of OTUs associated with γ-Proteobacteria and Firmicutes.

Decline in fish oil and fish meal availability has forced the aquaculture sector to investigate alternative and sustainable aquafeed ingredients. Despite that several studies have evaluated the effect of fish oil replacement in aquaculture fish species, there is a knowledge gap on the effects of alternative dietary lipid sources on the gut microbiota in early life stages of Salmo salar. The present study evaluated the influence of dietary administration of two different lipid sources (fish oil and vegetable oil) on the intestinal microbiota of first feeding Atlantic salmon (S. salar) up to 93 days post first feeding (dpff). The two diets used in this study, FD (fish oil diet) and VD (blend of rapeseed, linseed and palm oils diet), were formulated to cover the fish nutritional requirements. Apart from the lipid source, the rest of the feed components were identical in the two diets. Hindgut samples were collected at 0, 35, 65, and 93 dpff. Moreover, fertilized eggs, yolk sac larvae, rearing water and feed were also collected in order to assess a possible contribution of their microbiota to the colonization and bacterial succession of the fish intestines. To analyze the bacterial communities, amplicon sequencing was used targeting the V3–V4 region of the 16S rRNA gene. The findings indicate that feeding on either fish oil or vegetable oil-based diet, fish growth variables (mean wet weight and total length) did not differ significantly during the experiment (p > 0.05). No significant differences were also found between the two dietary groups, regarding their gut bacteria composition, after the analysis of the 16S rRNA sequencing data. Instead, gut microbiota changed with age, and each stage was characterized by different dominant bacteria. These operational taxonomic units (OTUs) were related to species that provide different functions and have been isolated from a variety of environments. The results also show little OTUs overlap between the host and rearing environment microbiota. Overall, this study revealed the occurrence of a core microbiota in early life of Atlantic salmon independent of the feed-contained oil origin.

The aim of this study is to investigate the effect of three daily fish feeding frequencies, two, four and eight times per day (FF2, FF4, and FF8, respectively) on growth performance of sea bass (Dicentrarchus labrax)and lettuce plants (Lactuca sativa) reared in aquaponics. 171 juvenile sea bass with an average body weight of 6.80 ± 0.095 g were used, together with 24 lettuce plants with an average initial height of 11.78 ± 0.074 cm over a 45-day trial period. FF2 fish group showed a significantly lower final weight, weight gain and specific growth rate than the FF4 and FF8 groups. Voluntary feed intake was similar for all the three feeding frequencies treatmens (p > 0.05). No plant mortality was observed during the 45-day study period. All three aquaponic systems resulted in a similar leaf fresh weight and fresh and dry aerial biomass. The results of the present study showed that the FF4 or FF8 feeding frequency contributes to the more efficient utilization of nutrients for better growth of sea bass adapted to fresh water while successfully supporting plant growth to a marketable biomass.

It is well known that the gut microbiome and its interaction with the host influence several important factors for fish health such as nutrition and metabolism. Diet is one of the main factors influencing the composition of the gut microbiome in reared fish. Microalgae, due to their high fatty acid content, appear to be a promising alternative for replacing fish oil in aquafeed. Thus, the aim of this work was to evaluate the effects of dietary microalgae blends as fish oil replacers οn the midgut bacterial microbiota of the gilthead sea bream ( Sparus aurata ). The control diet (FO) contained only fish oil as a source of lipids, EPA and DHA fatty acids, while three experimental diets were used where fish oil was replaced at 67% by one of the following microalgae biomass blends: Microchloropsis gaditana and   Isochrysis sp. ( Tisochrysis lutea ) (MI), Phaeodactylum tricornutum and   Isochrysis sp. (PI) and Schizochytrium sp.   and P. tricornutum (SP). The midgut bacterial community composition of the experimental diets was altered compared to the control diet. There were 11 operational taxonomic units (OTUs) that were highly abundant in FO compared to the three experimental diets (FO, MI, SP) and two OTUs that were found in high abundance in both FO and the experimental diets in all comparisons (FO-MI, FO-PI, FO-SP). Most of the highly abundant OTUs in the experimental diets were unique to each experimental diet, with two OTUs being found in common between FO-MI and FO-PI. Additional evidence from the presumptive bacterial functional metabolic pathways suggested that the microalgae-based diets resulted in one over-expressed and one under-expressed pathway. The overexpressed pathway was related to the metabolism of fucose, a major constituent of the polysaccharide content of several microalgal species. Peptidoglycan biosynthesis was the under-expressed metabolic pathway. This suggests that a new gut microbiota profile was selected due to the microalgae inclusion in the provided diet. This study showed that, with the absence of mortality in fish, the gilthead sea bream gut microbiome can smoothly adapt its function according to the metabolic capacity of the dietary microalgae combinations that were used. The MI feed seems to promote several beneficial bacteria with potential probiotic abilities in the fish gut, belonging to the Pseudoalteromonas, Pseudomonas, Bacillus and Rhodopseudomonas genera.