SSU rRNA sequencing data for bacterial communities of the mucosa and the gut contents of rainbow trout on a high-carbohydrate and high-protein diet
Description
The growing aquaculture industry requires more feed resources and the development of alternative feed formulations to replace costly fishmeal. Given the markedly large observed variability in the composition of the gut microbiota among fish populations, it is assumed that diet can significantly influence the bacterial communities of salmonids. This effect should be taken into account because intestine microbiota is known to be essential not only for the effective assimilation of food, but also for the functioning of the immune system of the fish. The data presented relate to the study of the possibility of changing the intestinal microbiome of carnivorous fish rainbow trout Oncorhynchus mykiss feed with an extremely high-carbohydrate diet in comparison with a high-protein diet based on fishmeal. Total DNA was isolated from these samples and used to produce v3-v4 SSU rRNA amplicons, which were then sequenced on Illumina MiSeq (2x300 bp) and assembled into 97% identity OTUs.The dataset provides information on the bacterial communities of the parietal microflora (autochthonous) of the rainbow trout intestine, as well as the composition of the chyme microbiota (allochthonous) depending on the fish diet. Table "OTUs" presents data on the composition of bacterial communities in the hindgut and foregut of farmed rainbow trout fed a high carbohydrate and high protein diet. OTUs that were present in only one of the samples or had no more than one read per sample were excluded as singletons. However, these OTUs were not removed from the taxonomy table. The "16s.otutab (1)" table is an unfiltered OTU table for readers wishing to reproduce the analysis with less stringent filtering criteria. The "Taxonomy" table contains a breakdown of the taxonomy of these unique OTUs. The resulting 16S rRNA gene sequencing data set provides insight into the distribution of bacteria between different parts of the intestine, as well as in the allochthonous and autochthonous microflora of trout.
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Steps to reproduce
For the experiment we used juvenile (0+) rainbow trout O. mykiss weighing 70-76 g. Trout juveniles were randomly divided into two groups (16 each) and distributed in two installations with a recirculating water supply system. In the first week of acclimation, the fish were not fed; in the second week, the fish were fed with the same food as on the fish farm Biomar No. 3 (Denmark) at the rate of 0.8% of body weight per day. After acclimation, the first group of fish began to receive experimental high-protein feed, while the second group received high-carbohydrate feed at the rate of 0.8% of body weight per day. Experimental batches of feed were made on an automatic line from Amandus Kahl (Germany). Diets were adjusted to be isoenergetic by crude lipids. Diets were supplemented with the same standard vitamin and mineral premix After 54 days of experiment, fish were anesthetized in the water clove oil suspension (0.5 ml/L). Next, the fish was dissected, observing the sterility of the sampling area. After dissection, fish intestines were tied with threads to separate the contents of the anterior and posterior sections. Each section of the intestine was opened in turn, and a food bolus was taken with sterile sticks, and the mucosa was scraped with a sterile scalpel, transferred into sterile cryotubes and frozen immediately in liquid nitrogen. Total DNA was isolated from samples using the DiaGene kit for DNA extraction from animal tissues (Diam Cat. no. 3488, Russia). The quality and quantity of DNA were measured on a SmartSpec spectrophotometer (Bio-Rad, USA) at a wavelength of 260 and 280 nm. Libraries were prepared for sequencing according to the protocol described in the 16S Metagenomic Sequencing Library Preparation manual (Part # 15044223 Rev. B; Illumina). The quality of the obtained genomic DNA samples was preliminarily checked by agarose gel electrophoresis. Amplification of the variable regions V3-V4 of the 16S rRNA gene was carried out using universal primers. After obtaining the amplicons, the libraries were purified and mixed equimolarly using the SequalPrep™ Normalization Plate Kit (ThermoFisher, Cat # A10510-01). The quality control of the obtained pools of libraries was carried out using the Fragment Analyzer system, quantitative analysis was carried out using qPCR. 3. The pool of resulting libraries was sequenced on Illumina MiSeq (read length - 300 bp on both sides of the fragments) using MiSeq Reagent Kit v3 (600 cycles). The resulting FASTQ files were generated using bcl2fastq v2.17.1.14 Conversion Software (Illumina). The resulting paired readings were collected into contigs. Low quality readers, unassembled pairs (producing contigs longer than 470 nucleotides) and chimeric readers were removed from the analysis. The remaining contigs were modified with the SSU rRNA reference alignment (SILVA v138.1 database). Tracks that were correctly aligned were used to create 97% of the Operational Taxonomic Units (OTUs).