Exploring early micronutrient deficiencies in rainbow Trout (Oncorhynchus mykiss) by next-generation sequencing technology--from black box to functional genomics

PLoS One. 2013 Jul 24;8(7):e69461. doi: 10.1371/journal.pone.0069461. Print 2013.


This work studies final nutritional status and transcriptional responses of rainbow trout (Oncorhynchus mykiss Walbaum 1792) (28 g) after a 10 week feeding experiment designed to elucidate the effect of adding a vitamin and mineral premix on growth, health, and nutritional endpoints. Juvenile fish were fed a either a diet supplemented with a vitamin and mineral premix (Diet S) or the same diet without premix supplementation (Diet U). The analyzed micronutrient composition of diets differed accordingly. Pooled livers from 15 fish from each dietary group were used to create suppression subtractive hybridization (SSH) cDNA libraries that were sequenced with 454 FLX GS Titanium Technology. In total 552 812 reads were sequenced from the two cDNA libraries. Ingenuity pathway analysis (IPA) was then used to characterize the hepatic transcriptome of the two dietary groups of rainbow trout. In the present communication we discuss how selected micronutrients may affect the transcriptome at suboptimal status by directly impacting the cellular metabolism, functions, and structures, and by introducing respective compensatory mechanisms. Processes related to lipid metabolism, peptide hydrolysis, oxygen transportation, and growth development were mostly affected. Considering the transcriptomics data relative to changes in nutritional status from the feeding study and the background phenotypic outcome of growth performance and gill histopathology, the outcome of the transcriptional profiling are suggested to be mainly related to suboptimal pantothenic acid and vitamin C nutrition.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • DNA, Complementary / genetics
  • Genomics / methods*
  • High-Throughput Nucleotide Sequencing / methods*
  • Micronutrients / deficiency*
  • Micronutrients / physiology
  • Oncorhynchus mykiss / genetics*
  • Oncorhynchus mykiss / physiology


  • DNA, Complementary
  • Micronutrients

Grant support

The biological material for this study was obtained in collaboration with BioMar AS (Trondheim, Norway) by Dr. Arne Guttvik and Dr. Kim Schön Ekmann (BioMar AS, Hirtshals, Denmark). This sideline project activity was financed by NIFES and partly connected to the EU-financed FP7 project ARRAINA. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.