Environmental and physiological factors shape the gut microbiota of Atlantic salmon parr (Salmo salar L.)

Abstract

Gut microbes are key players in host immune system priming, protection and development, as well as providing nutrients to the host that would be otherwise unavailable. Due to this importance, studies investigating the link between host and microbe are being initiated in farmed fish. The establishment, maintenance and subsequent changes of the intestinal microbiota are central to define fish physiology and nutrition in the future. In fish, unlike mammals, acquiring intestinal microbes is believed to occur around the time of first feeding mainly from the water surrounding them and their microbial composition over time is shaped therefore by their habitat. Here we compare the distal intestine microbiota of Atlantic salmon parr reared in a recirculating laboratory aquarium with that of age matched parr maintained in cage culture in an open freshwater loch environment of a commercial fish farm to establish the microbial profiles in the gut at the freshwater stage and investigate if there is a stable subset of bacteria present regardless of habitat type. We used deep sequencing across two variable regions of the 16S rRNA gene, with a mean read depth of 180,144 ± 12,096 raw sequences per sample. All individual fish used in this study had a minimum of 30,000 quality controlled reads, corresponding to an average of 342 ± 19 Operational Taxonomic Units (OTUs) per sample, which predominantly mapped to the phyla Firmicutes, Proteobacteria, and Tenericutes. The results indicate that species richness is comparable between both treatment groups, however, significant differences were found in the compositions of the gut microbiota between the rearing groups. Furthermore, a core microbiota of 19 OTUs was identified, shared by all samples regardless of treatment group, mainly consisting of members of the phyla Proteobacteria, Bacteroidetes and Firmicutes. Core microbiotas of the individual rearing groups were determined (aquarium fish: 19 + 4 (total 23) OTUs, loch fish: 19 + 13 (total 32) OTUs), indicating that microbe acquisition or loss is occurring differently in the two habitats, but also that selective forces are acting within the host, offering niches to specific bacterial taxa. The new information gathered in this study by the Illumina MiSeq approach will be useful to understand and define the gut microbiota of healthy Atlantic salmon in freshwater and expand on previous studies using DGGE, TGGE and T-RFPL. Monitoring deviations from these profiles, especially the core microbes which are present regardless of habitat type, might be used in the future as early indicator for intestinal health issues caused by sub optimal feed or infectious diseases in the farm setting.

Statement of relevance: The Microbiome is central to gut health, local immune function and nutrient up take. We have used deep sequencing approach to show differences in rearing conditions of Atlantic salmon. This work is of interest to aquaculture nutritionists.

Keywords: Atlantic salmon; Gut microbiota; Next-generation sequencing.

Fig. 1

Relative abundance (%) of main bacterial taxa found in digesta collected from the distal intestine of Atlantic salmon (Salmo salar) parr at phylum level (A) and genus level (B). Phyla and genera below an abundance of 0.1% are not shown but summarised in a mixed group “< 0.1% abundance”. Bacterial profiles are shown on an individual level, a rearing group level (aqua = recirculating aquarium system, loch = open loch environment) and on an overall level (= all).

Fig. 2

Operational Taxonomic Units (OTUs) of microbes identified in the distal intestine digesta of Atlantic salmon (Salmo salar) parr found to be significantly different between rearing groups (recirculating aquarium group and open loch environment group) by Metastats analysis (see Supplementary Tables 1 and 2). 634 OTUs were found to be entirely significantly present, of which 306 were significantly present in the aquarium group and 328 significantly present in the loch group. Furthermore 71 OTUs were found to show significantly different abundance between the observational groups, with 10 OTUs that were more abundant in the aquarium group and 61 OTUs that were more abundant in the loch group (see Supplementary Table 3). For a full list of OTUs found to differ significantly between observational groups refer to Supplementary Tables 1, 2 and 3.

Fig. 3

Core microbiota of distal intestine digesta in Atlantic salmon (Salmo salar) parr. Core microbiota was identified at an overall level (regardless of rearing group), and at a rearing group level (aqua = recirculating aquarium facility, loch = open loch environment).

Fig. 4

Multiple dimension scale (MDS) plots of unweighted (A) and weighted (B) UniFrac distances of distal intestine digesta microbiota found in Atlantic salmon (Salmo salar) parr by rearing group. Beta diversity analysis of unweighted UniFrac (A, presence/absence of Operational Taxonomic Units (OTUs)) was found significantly different between observational groups (PERMANOVA, Pseudo F-statistic 1.4599, P = 0.006, based on 999 permutations). However, analysis of weighted UniFrac (B, presence/absence/abundance of OTUs) was not found significantly different (PERMANOVA, Pseudo F-statistic 0.9589, P = 0.419, based on 999 permutations). Red = recirculating aquarium facility, blue = open loch environment.