Among other factors, nutrition is one of the most determining factors in fish farming, representing 40–70% of the production costs and determining survival, growth potential and quality of fish. The proper development of nutritionally balanced diets relies on multifactorial and multidisciplinary studies to fulfill species- and stage-specific nutritional requirements. However, since each nutrient might have different roles (and requirements) depending on the tissue and biological process considered, the use of integrative biomarkers as hall mark of the global condition of farmed fish might be a powerful tool to improve feed formulation and fish physiology monitoring. Here, the use of circulating non-coding RNAs (ncRNAs) found in blood plasma from rainbow trout (O. mykiss) as integrative biomarkers was explored.
We studied the population of miRNAs as biomarkers of fish physiology when they were fed with diets formulated base on different alternative raw materials during > 60 days or under feeding/fasting conditions during 10 days or (Experiment 2).
In Exp. 1, miRNAs were isolated from 12 (6 from fish fed on diets containing fish meal (FM) and 6 from FM devoid diets) samples, while in Exp. 2 we studied 8 (4 from fed and 4 from unfed fish) samples, using the miRNeasy Serum/Plasma Kit. Library preparation was performed using < 100 ng of ncRNA, normalized and sequenced in an Illumina platform (single-end, 51 cycles).
Raw reads were bioinformatically processed and mapped/annotated against Salmo salar known miRNAs from miRBase v22.1/RNAcentral 14.0 databases. Novel miRNAs were predicted with miRDeep2 using USDA_OmykA_1.1 genome as reference. SnoRNAs, rRNAs and tRNAs were also found. An example of the output from Exp. 1 is presented in Table 1.
We will list the identified miRNAs being found differentially expressed in both experiments and the potential molecular pathways post-transcriptionally regulated by them. Using this approach, we were able get further insights on how diet and feeding regime might alter the expression of these miRNAs in blood plasma, and the potential physiological consequences.
Acknowledgments: This work was funded by MET2VI project (Ref. RTI2018-099029-A-I00) from European Regional Development Fund (ERDF)—MICIU—AEI; CONACYT post-doc fellowship 2019–000012-01EXTV-00292; and Ramón y Cajal contract (RYC2018-025337-I) from MICIU and the European Social Fund, “The European Social Fund invests in your future” through the. Authors also thanks the support from the network LARVAplus (117RT0521) funded by the CYTED.