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Understanding the evolutionary relationships between a host and its intestinal resident bacteria can transform how we understand adaptive phenotypic traits. The interplay between hosts and their resident bacteria inevitably affects the intestinal environment and, thereby, the living conditions of both the host and the microbiota. Thereby this co-existence likely influences the fitness of both bacteria and host. Whether this co-existence leads to evolutionary co-diversification in animals is largely unexplored, mainly due to the complexity of the environment and microbial communities and the often low host selection. We present the gut metagenome from wild Atlantic salmon (Salmo salar), a new wild organism model with an intestinal microbiota of low complexity and a well-described population structure, making it well-suited for investigating co-evolution. Our data reveal a strong host selection of a core gut microbiota dominated by a single Mycoplasma species. We found a clear co-diversification between the population structure of Atlantic salmon and nucleotide variability of the intestinal Mycoplasma populations conforming to expectations from co-evolution between host and resident bacteria. Our results show that the stable microbiota of Atlantic salmon has evolved with its salmonid host populations while potentially providing adaptive traits to the salmon host populations, including defence mechanisms, biosynthesis of essential amino acids, and metabolism of B vitamins. We highlight Atlantic salmon as a novel model for studying co-evolution between vertebrate hosts and their resident bacteria. [Figure not available: see fulltext.].

Understanding the evolutionary relationships between a host and its intestinal resident bacteria can transform how we understand adaptive phenotypic traits. The interplay between hosts and their resident bacteria inevitably affects the intestinal environment and, thereby, the living conditions of both the host and the microbiota. Thereby this co-existence likely influences the fitness of both bacteria and host. Whether this co-existence leads to evolutionary co-diversification in animals is largely unexplored, mainly due to the complexity of the environment and microbial communities and the often low host selection. We present the gut metagenome from wild Atlantic salmon (Salmo salar), a new wild organism model with an intestinal microbiota of low complexity and a well-described population structure, making it well-suited for investigating co-evolution. Our data reveal a strong host selection of a core gut microbiota dominated by a single Mycoplasma species. We found a clear co-diversification between the population structure of Atlantic salmon and nucleotide variability of the intestinal Mycoplasma populations conforming to expectations from co-evolution between host and resident bacteria. Our results show that the stable microbiota of Atlantic salmon has evolved with its salmonid host populations while potentially providing adaptive traits to the salmon host populations, including defence mechanisms, biosynthesis of essential amino acids, and metabolism of B vitamins. We highlight Atlantic salmon as a novel model for studying co-evolution between vertebrate hosts and their resident bacteria. [Figure not available: see fulltext.].

Assessing the availability of dietary micro-minerals is a major challenge in mineral nutrition of fish species. The present article aims to describe a systematic approach combining different methodologies to assess the availability of zinc (Zn) in Atlantic salmon (Salmo salar). Considering that several Zn chemical species can be present in an Atlantic salmon feed, it was hypothesised that Zn availability is influenced by the Zn chemical species present in the feed. Thus, in this study, the first protocol is about how to extract the different Zn chemical species from the feed and to analyze them by a size exclusion chromatography-inductively coupled plasma mass spectroscopy (SEC-ICP-MS) method. Subsequently, an in vitro method was developed to evaluate the solubility of dietary Zn in Atlantic salmon feeds. The third protocol describes the method to study the impact of changing Zn chemical species composition on the uptake of Zn in a fish intestinal epithelial model using a rainbow trout gut cell line (RTgutGC). Together, the findings from the in vitro methods were compared with an in vivo study examining the apparent availability of inorganic and organic sources of Zn supplemented to Atlantic salmon feeds. The results showed that several Zn chemical species can be found in feeds and the efficiency of an organic Zn source depends very much on the amino acid ligand used to chelate Zn. The findings of the in vitro methods had less correlation with that outcome of the in vivo study. Nevertheless, in vitro protocols described in this article provided crucial information regarding Zn availability and its assessment in fish feeds.

The impact of dietary manganese (Mn) levels and sources on the growth and mineral composition of post-smolt Atlantic salmon (Salmo salar) fed practical diets was studied. Seven experimental diets were prepared with graded supplementation level of Mn; basal diet had a Mn concentration of 15 mg kg−1, four diets with 5, 15, 35 and 65 mg kg−1 supplementation of Mn as MnSO4 and two diets with at 5 and 15 mg kg−1 supplementation of Mn as Mn-glycine (Mn-gly). Atlantic salmon (initial weight, 307 ± 25 g) were distributed to 21 tanks (35 fish/tank). These fish were randomly fed with one of the experimental diets, in triplicate groups to apparent satiation for 8 weeks. At week 4 and 8, samples of whole body, plasma, bile, liver and vertebrae were collected, and their mineral concentration determined. At week 8, feaces were collected by stripping for measuring apparent availability coefficient (AAC). Neither the Mn inclusion level, nor the source had a significant impact on growth and other performance indicators. Plasma and bile Mn concentrations were significantly affected by dietary treatments at both sampling points, at week 4 and 8; whereas, whole body, liver and vertebrae responded significantly only at the end of 8 weeks. Dietary Mn level needed to meet the requirement of post-smolt Atlantic salmon was estimated by non-linear regression models using saturation of whole body or tissue Mn status as response criteria. The estimates based on Mn concentration in whole body, vertebrae, plasma and apparent availability were 29.5 ± 5.3, 26.2 ± 2.7, 26.3 ± 4.9 and 34 ± 3.4 mg Mn kg−1 diet, respectively. Analysis of relative bioavailability index showed that low inclusion of Mn-gly (5 mg kg−1 supplementation) was 2.6 to 4.5-fold more efficient than MnSO4 to attain whole body or tissue Mn saturation levels. On the contrary, high inclusion of Mn-gly (15 mg kg−1 supplementation) reduced the AA