An estimate of relative abundance of specific bacterial groups in samples was calculated by dividing their count on specific medium by that of total viable count selleck chemicals (LH) of each respective sample. This was done to compare the relative abundance of cultivated bacteria to those obtained via 16S rRNA analysis. DNA extraction During the shelf life

trials, fractions of tenfold diluted fish samples were collected and kept at -80°C until DNA extraction. Raw material and 20 storage trial samples were selected for 16S rRNA analysis. Template genomic DNA was isolated from one ml of these diluted samples as described before [44]. The sample was centrifuged at 11000 × g for 7 min to form a pellet. The supernatant was discarded and DNA was recovered from the pellet using Promega Magnesil KF, Genomic system (MD1460) DNA isolation kit (Promega Corporation, Madison, USA) in combination with KingFisher magnetic beads automatic DNA isolation instrument (Thermo Labsystems, Waltham, USA). 16S rRNA analysis The raw material and two samples from each treatment were selected for DNA analysis, from early storage (days 6-7) and late storage (13-15 in air samples and 21-28 in MA samples) resulting in a total of 21 samples. The PCR reaction was done by

amplifying the 16S rRNA gene with universal primers, 9F and click here 1544R (5′-GAGTTTGATCCTGGCTCAG-3 and ’5-CCCGGGATCCAAGCTTAGAAAGGA-3′ respectively). PCR reaction conditions, cloning and sequencing of the PCR products obtained from the cod samples was performed essentially as described before [45]. Sequencing was performed directly after the PCR reaction. Partial sequencing was performed with R805 primer; ’5-GACTACCCGGGTATCTAATCC-3′ resulting in 500-600 bp read length. The species coverage by the 16S analysis was estimated using the equation where C is coverage, n1 is the number of unpaired sequences (number of sequences that did not group with any other in the annealing) and Nt is the number of total clones analyzed. Multiple alignments were carried out using ClustalW

(v.1.83) and subsequent phylogenetic dendrogram of the 16S rRNA was plotted with the neighbour-joining software using NjPlot. Protirelin Terminal restriction fragment length polymorphism (t-RFLP) Extracted DNA from duplicate samples was pooled prior to PCR for the t-RFLP analysis. The PCR was performed with 9F forward primer (sequence above) with a 5′ FAM terminal label and HEX labelled reverse primer 805R. The labelled PCR products were digested with HaeIII and AluI (Fermentas, Hanover, MD, USA) in a 10 μL reaction volume for 2 h. The digested PCR product was diluted 1:20 and 2 μL added to 8 μL of GeneScan 500 LIZ internal size standard (Applied Biosystems, Warrington, UK) in formamide. The fragment analysis was carried out in ABI3730 DNA analyzer. A peak in the chromatogram, here after called terminal restriction fragment (t-RF), is regarded as one taxonomic unit. Data analysis was carried out on the GeneMapper software (v.4.