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 relevanceThe 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.

The malleable gut microbiome of juvenile rainbow trout (Oncorhynchus mykiss): Diet-dependent shifts of bacterial community structures

“…Since the focus of this study was not to evaluate individual protein sources, but the nutritional programming effect of first feeding diets, specific differences to other studies could also result from the used protein sources. The observed phyla in general were however quite consistent with previous results found for salmonids [51, 56, 64]. The core microbiome analysis performed in the present study demonstrated that fish fed either a fishmeal or a plant-protein based diet only share two OTUs after the first feeding period and none at the end of the second feeding period.…”

Application of molecular tools to elucidate the microbiota of seafood

“…; Dehler et al . ). As a result, novel culture‐independent technologies have emerged as an opportunity to better understand this microbiota (Lan and Love ; Larsen et al .…”

“…Thus, the Illumina MiSeq platform approach is also useful in understanding and defining the intestinal microbiota of Atlantic salmon and has expanded previous studies performed by DGGE, TGGE and T‐RFPL (Dehler et al . ).…”

“…Dehler et al . () used the Illumina MiSeq platform for the sequencing of the variable 16S rRNA regions of Atlantic salmon ( Salmo salar L.) gut microbiota, evaluating 12 individuals in aquaria and eight in ponds. After filtering the crude sequencing results (3 602 871 readings), 3 226 813 sequences were obtained, with a mean of 161 341 ± 12 472 sequences and a total of 342 ± 19 OTUs per sample.…”

“…; Dehler et al . ; Lee et al . ), and present several advantages, such as high sensitivity, specificity and speed in obtaining results (Janda and Abbott ; Ceuppens et al .…”