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

Vibrio species' infections are a common sequelae to environmental stress or other disease processes in shrimp, but the mechanism by which the shrimp eliminate the bacteria is poorly understood. In this study, the penetration, fate and the clearing of V. vulnificus were investigated in Penaeus monodon. A bacterial disease isolate from a shrimp farm was identified as V. vulnificus biotype I. Polyclonal antiserum was raised in rabbits against the bacterium and the specificity was verified by ELISA and immunoblot against a range of Vibrio spp. and other Gram-negative bacteria. The bacteria were then administered to P. monodon juveniles by injection, immersion and oral intubation. An indirect immunoperoxidase technique was employed in a time course study to follow the bacteria and bacterial antigens in the tissue of the shrimp. Bacteria were cleared by a common route, regardless of the method of administration. Observations in immersion challenge were similar to a combination of those for oral and injection challenges. With immersion, bacteria entered the shrimp through damaged cuticle or via insertion points of cuticular setae. Shortly after entry, whole bacterial cells were observed in the haemolymph and connective tissue. They were either phagocytosed by haemocytes, or broken down outside host cells. Haemocytes containing bacterial cells or antigens (HCB) were observed in the connective tissue and haemolymph. HCB accumulated around the hepatopancreas, midgut, midgut-caecum, gills, heart and lymphoid organ. Free bacterial antigens also accumulated in the heart and lymphoid organ. Bacteria entering through the mouth by oral intubation or immersion were broken down so that only soluble or very fine particles entered the hepatopancreas. Bacterial antigens passed through the hepatopancreas into the haemolymph. Antigens were initially observed in the haemolymph sinuses and subsequently accumulated in the heart and lymphoid organ. Bacterial antigens were released from the shrimp, initially through the gills and subsequently through hepatopancreatic B-cells, branchial podocytes and sub-cuticular podocytes. KEY WORDS: Shrimp · Vibrio · Penaeus monodonResale or republication not permitted without written consent of the publisher

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The live marine baitworm trade harvests, packages, and ships polychaete worms and packing algae (wormweed) from Maine, USA to consumers globally, inadvertently transferring numerous invertebrates that naturally occur in the algal habitat. Here, we use a focal taxa, the globally invasive European green crab Carcinus maenas, to examine costs associated with the successful introductions via this vector and suggest an alternative packaging, already in use in Europe. We show that restricting the use of wormweed at the source could solve the problem of transferring hitchhikers without a change in product cost. However, to the extent that baitworms in wormweed are what US consumers are accustomed to receiving, alternative packing might restrict demand for baitworms, lower producer prices, and reduce quantities traded. Avoiding such economic costs and receiving the benefits of reduced likelihood of unwanted invasion at low or no cost to producers should be of interest to policymakers and practitioners tasked with protecting ecosystems.