title: Phylogenetic and functional characterization of the distal intestinal microbiome of rainbow trout Oncorhynchus mykiss from both farm and aquarium settings.
abstract: OBJECTIVE
  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.
  
  
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Institute of Aquaculture, University of Stirling, Stirling, UK.
authors.forename: P P
authors.initials: PP
authors.lastname: Lyons
authors.affiliation: Institute of Aquaculture, University of Stirling, Stirling, UK.
authors.forename: J F
authors.initials: JF
authors.lastname: Turnbull
authors.affiliation: Alltech Biotechnology Inc., Nicholasville, KY, USA.
authors.forename: K A
authors.initials: KA
authors.lastname: Dawson
authors.affiliation: Institute of Aquaculture, University of Stirling, Stirling, UK.
authors.forename: M
authors.initials: M
authors.lastname: Crumlish
mesh_terms: D000818:Animals; D017756:Aquaculture; D001419:Bacteria / Q000145:classification* / Q000235:genetics; D005618:Fresh Water; D000069196:Gastrointestinal Microbiome; D007422:Intestines / Q000382:microbiology*; D017686:Oncorhynchus mykiss / Q000382:microbiology*; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics
chemical_list: D012336:RNA, Ribosomal, 16S
keywords: aquaculture; diversity; intestinal microbiology; metabolism; metagenomics