Aims This study focused on comparing the phylogenetic composition and functional potential of the intestinal microbiome of rainbow trout sourced from both farm and aquarium settings. Methods and Results Samples of distal intestinal contents were collected from fish and subjected to high throughput 16S rRNA sequencing, to accurately determine the composition of the intestinal microbiome. The predominant phyla identified from both groups were Tenericutes, Firmicutes, Proteobacteria, Spirochaetae and Bacteroidetes. A novel metagenomic tool, PICRUSt, was used to determine the functional potential of the bacterial communities present in the rainbow trout intestine. Pathways concerning membrane transport activity were dominant in the intestinal microbiome of all fish samples. Furthermore, this analysis revealed that gene pathways relating to metabolism, and in particular amino acid and carbohydrate metabolism, were upregulated in the rainbow trout intestinal microbiome. Conclusions The results suggest that the structure of the intestinal microbiome in farmed rainbow trout may be similar regardless of where the fish are located and hence could be shaped by host factors. Differences were, however, noted in the microbial community membership within the intestine of both fish populations, suggesting that more sporadic taxa could be unique to each environment and may have the ability to colonize the rainbow trout gastrointestinal tract. Finally, the functional analysis provides evidence that the microbiome of rainbow trout contains genes that could contribute to the metabolism of dietary ingredients and therefore may actively influence the digestive process in these fish. Significance and Impact of the Study To better understand and exploit the intestinal microbiome and its impact on fish health, it is vital to determine its structure, diversity and potential functional capacity. This study improves our knowledge of these areas and suggests that the intestinal microbiome of rainbow trout may play an important role in the digestive physiology of these fish.

This is the peer reviewed version of the following article: Lyons, P. P., Turnbull, J. In this study, high throughput 16S rRNA sequencing was used to investigate the effect of a 171Samples were allowed to settle, and total genomic DNA was extracted and purified using the 192Illumina libraries were prepared following the method described by Caporaso, Lauber, Walters, All fish consumed both diets readily and upon conclusion of the trial, the weighed individuals 273 from the treatment group had a higher mean weight and condition factor than the control group. 274The final mean weight and condition factor (± SE) for the treatment group was 136.6 ± 12.1g 275 and 1.44 ± 0.06 whereas these values for the control group were 116.5 ± 9.3g and 1.33 ± 0.04 276 respectively ( Figure S1). A t-test was performed using the Minitab 15 statistical software to 277 test for significant differences between the performance parameters for both groups, however 278 no such differences were found (p = 0.107). Sequence data and diversity analyses 280After quality filtering of sequences, a total of 18,282,541 sequences remained for analysis, The overall microbial community composition was similar in both the control and treatment 296 populations of fish. The distribution of OTU's at the phylum level of both the control and 297 treatment libraries is illustrated below (Figure 1). The vast majority of reads were assigned to 298 nine separate bacterial phyla, although an overall total of 13 phyla were recorded. Within these 299 phyla, 13 microbial classes dominated (Figure 2 is still yet to be fully characterized. 329Principal coordinate analyses, when visualized based on the thetaYC distance matrix 330 comparing similarities in community structure, showed that samples were broadly 412The Tenericutes were the dominant microbial phylum in the vast majority of samples, followed

In this study, next generation sequencing (NGS) was used to survey the 16S rRNA ribotypes of the distal intestinal lumen and mucosal epithelium of farmed rainbow trout. This approach yielded a library consisting of 2 979 715 quality filtered paired sequences, assigned to genus level of taxonomy using the Ribosomal Database Project (RDP). A high level of diversity was observed in both regions. A total of 90 bacterial genera were identified in the lumen of all fish sampled, compared with 159 in the mucosa. The allochthonous microflora was dominated by sequences belonging to the c Proteobacteria (mean sequence abundance 54.3%), in particular the Enterobacteriaceae, with Yersinia, Serratia, Hafnia and Obesumbacterium the most abundant genera. Fewer c Proteobacteria (mean sequence abundance 37%) were present in the mucosa, and autochthonous communities consisted of a more even split among the bacterial classes, with increases in sequences assigned to members of the b Proteobacteria (mean sequence abundance 18.4%) and Bacilli (mean sequence abundance 16.8%). The principal bacterial genera recorded in the mucosa were Cetobacterium, Yersinia, Ralstonia, Hafnia and Carnobacterium. The results of this study demonstrate that the luminal and mucosal bacterial communities may be different in their respective structures, and that the mucosal microflora of rainbow trout may be more diverse than previous research has suggested. This research also demonstrated a degree of conservation of bacterial genera between individual fish sampled, and is to the author's knowledge the first time the MiSeq ® NGS platform has been used to explore the rainbow trout intestinal microflora.

Atlantic salmon are a species of major economic importance. Intense innovation is underway to improve salmon feeds and feed additives to enhance fish performance, welfare, and the environmental sustainability of the industry. Several gut models targeted at monogastric vertebrates are now in operation. Here we report progress in the development of an Atlantic salmon in vitro gut model, SalmoSim, to simulate three gut compartments (stomach, pyloric caecum and mid gut) and associated microbial communities. The artificial gut model was established in a series of linked bioreactors seeded with biological material derived for adult marine phase salmon. In biological triplicate, the response of the in vitro system to two distinct dietary formulations (fish meal and fish meal free) was compared to a parallel in vivo trial over forty days. 16S rDNA sequencing, qPCR, ammoniacal nitrogen and volatile fatty acid measurements were undertaken to survey microbial community dynamics and function. SalmoSim communities were indistinguishable (p=0.230) from their founding inocula at 20 days and most abundant genera (e.g. Psycrobacter, Staphylococcus, Pseudomonas) proliferated the in vitro system. Real salmon and SalmoSim responded similarly to the introduction of the novel feed, with most taxa (96% Salmon, 97% SalmoSim) unaffected, while a subset of taxa was affected non-identically across both systems. Consistent with a low impact of the novel feed on microbial community function, VFA profiles were not significantly different in SalmoSim pre and post the switch feed. This study represents an important first-step in the development of an in vitro gut system as a tool for the improvement of salmon nutrition.