title: Differential responses of the gut transcriptome to plant protein diets in farmed Atlantic salmon.
abstract: BACKGROUND
  The potential for alternative plant protein sources to replace limited marine ingredients in fish feeds is important for the future of the fish farming industry. However, plant ingredients in fish feeds contain antinutritional factors (ANFs) that can promote gut inflammation (enteritis) and compromise fish health. It is unknown whether enteritis induced by plant materials with notable differences in secondary metabolism is characterised by common or distinct gene expression patterns, and how using feeds with single vs mixed plant proteins may affect the gut transcriptome and fish performance. We used Atlantic salmon parr to investigate the transcriptome responses of distal gut to varying dietary levels (0-45%) of soy protein concentrate (SPC) and faba bean (Vicia faba) protein concentrate (BPC) following an 8-week feeding trial. Soybean meal (SBM) and fish meal (FM) were used as positive and negative controls for enteritis, respectively. Gene expression profiling was performed using a microarray platform developed and validated for Atlantic salmon.
  
  
  RESULTS
  Different plant protein materials (SPC, BPC and SBM) generated substantially different gut gene expression profiles, with relatively few transcriptomic alterations (genes, pathways and GO terms) common for all plant proteins used. When SPC and BPC were simultaneously included in the diet, they induced less extensive alterations of gut transcriptome than diets with either SPC or BPC singly, probably due to reduced levels of individual ANFs. The mixed plant protein diets were also associated with improved body composition of fish relative to the single plant protein diets, which may provide evidence for a link between the magnitude of changes in gut transcriptome and whole-animal performance.
  
  
  CONCLUSIONS
  Our results indicate that gut transcriptomic profiling provides a useful tool for testing the applicability of alternative protein sources for aquaculture feeds and designing diets with reduced impact of ANFs on fish health. Ultimately, understanding diet-gut interactions and intestinal homeostasis in farmed fish is important to maximise performance and to ensure that aquaculture continues to be a sustainable source of food for a growing world population.
authors.affiliation: Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 2TZ, UK. e.krol@abdn.ac.uk.
authors.forename: Elżbieta
authors.initials: E
authors.lastname: Król
authors.affiliation: Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 2TZ, UK. a.douglas@abdn.ac.uk.
authors.forename: Alex
authors.initials: A
authors.lastname: Douglas
authors.affiliation: Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA, UK. d.r.tocher@stir.ac.uk.
authors.forename: Douglas R
authors.initials: DR
authors.lastname: Tocher
authors.affiliation: EWOS Innovation AS, Dirdal, Norway. Viv.Crampton@ewos.com.
authors.forename: Viv O
authors.initials: VO
authors.lastname: Crampton
authors.affiliation: Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 2TZ, UK. j.speakman@abdn.ac.uk.
authors.forename: John R
authors.initials: JR
authors.lastname: Speakman
authors.affiliation: Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 2TZ, UK. c.secombes@abdn.ac.uk.
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Secombes
authors.affiliation: Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 2TZ, UK. sam.martin@abdn.ac.uk.
authors.forename: Samuel A M
authors.initials: SA
authors.lastname: Martin
mesh_terms: D000821:Animal Feed / Q000032:analysis*; D000824:Animal Nutritional Physiological Phenomena; D000818:Animals; D017756:Aquaculture; D020869:Gene Expression Profiling; D007413:Intestinal Mucosa / Q000378:metabolism; D010641:Phenotype; D014674:Plant Proteins, Dietary / Q000737:chemistry*; D020317:Salmo salar / Q000378:metabolism*; D013025:Glycine max / Q000737:chemistry; D059467:Transcriptome; D031307:Vicia faba / Q000737:chemistry
chemical_list: D014674:Plant Proteins, Dietary