In the present study, we characterize the gut bacterial communities of S. salar populations during early development (13 weeks of feeding) and fed two diets with different lipid source (FD, VD). Moreover, we characterized the bacterial communities from the rearing environment (rearing water and feeds) and the epibiotas of fertilized eggs and yolk sac larvae to determine their contribution in the bacterial colonization and succession of the gut. Previous studies suggest that the bacterial communities of the rearing environment, mainly from the rearing water and the feed, are important sources for community assembly of the intestinal microbiota of fish [12, 32–37]. For example, Schmidt et al. , reported a significant effect on intestinal microbial communities in postsmolt S. salar following replacement of dietary fishmeal with plant ingredients. However, the results in the present study suggest that substitution of fish oil by vegetable oils did not significantly affect the composition of intestinal microbial communities in the same host species.
The results of the present study indicate little relationship between the epibiotic, gut and water bacterial communities, whereas the life stage appeared to be the main factor affecting the structure of gut microbiota. These results are in agreement with previous findings from Llewellyn et al. , who studied 96 wild-caught individuals of S. salar with different age and habitats, and observed grouping of their intestinal bacterial communities based on the lifecycle stage. In addition, Lokesh et al. , reported stage specific microbial enrichment in intestinal mucosa of S. salar (samples from embryonic stages up to 80-week post hatch). Similar stage specific signatures have also been reported across development in Sparus aurata , Danio rerio  and Gadus morhua  supporting further that the life stage seems to be the primary force shaping gut microbiota in juveniles’ stages of fish. The change in microbiota with life stage can be due to both host-microbe (e.g. development in morphology and immune system) and microbe-microbe interactions (mutualism, competitions and antagonism). The significance of these factors are, however, still not known.
Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes were the dominant bacterial phyla detected in S. salar samples for both dietary treatments in our study. This bacterial phylla seem to characterize the bacterial communities in individuals of Atlantic salmon (S. salar) at the freshwater life cycle stages . These bacterial phyla are also commonly found in the gut bacterial communities of both saltwater and freshwater fish species [3 − 9, 16–21, 29, 32–42]
Despite the fact that the two experimental feeds contained almost exclusively Firmicutes, the increase in relative abundance of Firmicutes in S. salar samples after the onset of feeding was not solely due to feed specific OTUs. It should also be noted that 26.4% of the bacterial representatives detected on fertilized eggs (EG) were not detected in the water of the incubation tank (WST). This support the view that the microbial communities of fish eggs may be vertically transmitted from their parents or horizontally from their breading tank [38, 43].
In agreement with previous studies [5, 19, 38], the observed species richness in water samples was always an order of magnitude higher than the richness of the host samples. Bacterial communities in rearing water did not show major shifts during the experiment. OTU0001 dominated at all time points, with closest relative the bacterial species Polynucleobacter necessaries. This species is commonly found in freshwater samples and it can contribute to the catabolism of urea and reduction of nitrate . The dominant bacterial species in S. salar samples are related with bacterial species from various habitats. The dominant OTU on fertilized eggs (OTU0011) was classified within the Methylotenera genus (β-Proteobacteria) and has previously been detected in fertilized salmon eggs by Lokesh et al. . This genus consists of methylotrophic species that use methylamine as sole carbon, energy and nitrogen source . The dominant OTU at the YS stage (OTU0013), seems to be related with Delftia acidovorans (β-Proteobacteria). Species of the genus Delftia are obligate anaerobes, organotrophic and non-fermentative organisms (46). They have previously been detected in the gut of healthy individuals of Epinephelus coioides , Oncorhynchus mykiss  and Sparus aurata [29, 40] and S. salar .
Just before onset on feeding (D0), the dominant OTU (OΤU0009) showed similarities with the species Iodobacter fluviatilis of the Chitinibacteraceae (β-Proteobacteria) family. Species of this genus have been recorded mainly in sediment and water samples [50–52]. Their presence on fish skin (Oncorhynchus mykiss and Salmo trutta) has been associated with skin lesions . However, the species has previously been detected in high relative abundance in healthy Coreius guichenoti individuals  whereas the present study reports the presence of this bacterial species in S. salar gut microbiota for the first time.
After first feeding, although not statistically significant, differences were found between the bacterial communities in gut, each stage was characterized by different dominant OTUs. Moreover, gut bacterial communities differed also between dietary treatments regarding their dominant bacterial species (OTU). Chitinibacteraceae, the dominant bacterial family on D0, (with relative abundance 32.3%), was detected in ~ 50x lower relative abundance (≤ 0.6%) in the rest of the samples. At D35F and D65F, the dominant OTUs (OTU0017 and OTU0070, classified as Pseudomonas viridiflava and Janthinobacterium agaricidamnosum, respectively), are described as plant [55–58] and mushroom pathogens [59–60]. According to recent findings, Janthinobacterium lividum (β-Proteobacteria) produce antimicrobial activity against multidrug resistant bacteria of clinical and environmental origin, such as Enterococci and Enterobacteriaceae . Its presence in the gastrointestinal bacterial communities of S. salar, may have probiotic activity.
At D35 and D65 samples from the VD dietary treatment were dominated by OTU0005, with closest relative Cloacibacterium normanense (Bacteroidetes). This OTU was also dominant at D93F. According to the literature, this species is frequently present in sewage treatment plants [62, 63] where it contributes in decomposition of complex organic compounds . Similar processes may take place in the intestinal system of S. salar at D35V, D65V and D93F. The dominant OTU at D93V (OTU0004), also dominant in the provided feed (FD, VD), was affiliated with Weissella cibaria (Firmicutes). This bacterial species belongs to the lactic acid bacteria, and has antimicrobial activity in the intestinal system of other fish species . Other Weissella spp. have been found in gut of Oncorynchus mykiss  and S. salar [7–69]. It is worth noting that beside OTU0004, also OUT0013 and OTU0017 are associated with probiotic bacterial species (detected in all time points studied here, from EG to D93, independently of the dietary treatment, FD & VD). This observation suggests a co-evolutionary relationship of these bacterial species with the host studied here (S. salar), and a possible specialized function in the hosts intestinal system.