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Background  Microbial analyses performed in connection with the post-slaughter environment of farmed Atlantic salmon ( Salmo salar  L.) have mostly focused on specific bacteria that may have negative effects on the health of consumers. However, bacteria may also affect other quality variables. The objective of this study was to provide general knowledge about composition and dynamics of the bacterial communities present at slaughter and cold storage of farmed Atlantic salmon, as well as reveal any possible correlations to gelatinase activity, which may affect fillet quality. Thus, these data may provide a basis for optimization opportunities in the aquaculture industry.    Methods  Samples were taken from the digestive system harvested from 15 salmon immediately after slaughter. Another 17 salmon were taken from the processing line just before the final cleaning stage; of these eight were distributed in three iced storage boxes while the other nine were rinsed an extra time with industrial water before being distributed into another three storage boxes. In the following 6 days, samples were taken of skin mucus, liquids in the abdominal cavity and the storage ice. The compositions of the bacterial communities were analyzed by next-generation sequencing and gelatinase activity was measured in all samples except the storage ice.    Results  The bacterial communities in the digestive tract samples were dominated by the family  Mycoplasmataceae.  The genus  Aliivibrio  was also relatively abundant. Bacterial communities in the abdominal cavity were generally more diverse than the intestinal samples. However, all of the abdominal samples from storage box no. 3 had a high relative abundance of  Mycoplasmataceae , and could not be distinguished from the intestinal samples ( Q  = 1.27,  p  = 0.633) while being significantly different from the other abdominal samples ( Q  = 9.02,  p  = 0.01). In addition, the abdominal samples from storage box no. 3 had a significantly higher gelatin degrading activity ( Q  = 9.43,  p  = 0.001) than those from the other storage boxes and similar to the high gelatinase activity in the intestinal samples. This indicated that in storage box no. 3 there was a transfer of intestinal fluids to the abdominal cavities, which was not removed by the cleaning procedure. There was a significant difference of the major phyla detected in the skin mucus of salmon rinsed an additional time, as these salmon had a higher relative amount of  Firmicutes  ( F  = 4.76,  p  = 0.04) and lower amount of  Proteobacteria  ( F  = 4.41,  p  = 0.047).    Conclusions  The study showed a correlation between intestinal fluids and bacteria left in the abdominal cavity and gelatinase activity. This suggested that intestinal fluids and/or bacteria could enhance the degradation of connective tissue in the abdominal cavity and hence negatively affect the fillet quality. In addition, the study provided general knowledge of the composition and dynamics of bacterial communities present.

peerj

Composition and dynamics of the bacterial communities present in the post-slaughter environment of farmed Atlantic salmon (<i>Salmo salar</i>L<i>.</i>) and correlations to gelatin degrading activity

Composition and dynamics of the bacterial communities present in the post-slaughter environment of farmed Atlantic salmon (Salmo salarL.) and correlations to gelatin degrading activity