Microbial community analysis in brown shrimp (Crangon crangon) through cultivation dependent and independent (DGGE) method.

Like all seafood, fresh shrimp is perishable and should either be consumed or preserved. Microbiological (quality) control of fresh fish and shellfish is necessary for the determination of the remaining shelf-life and important for food safety. In this study the dominant microbiota of brown shrimp (Crangon crangon) was determined after boiling under various conditions and was also systematically identified during storage under different conditions without the addition of preservatives. A comparison was made with the microbiota present in shrimp samples stored with preserving agents. Freshly caught shrimp were analyzed microbiologically before processing and further processed on board the fishing vessel under the best possible hygienic conditions, unpeeled and manually (sterile) peeled, then stored under different conditions until microbiologically spoiled. Results were compared with industrially processed shrimp. Some of the freshly caught shrimp were kept alive and processed within 24 hour in the laboratory. The effect on the microbiological quality of various boiling parameters namely boiling time and temperature, concentration of salt, mass ratio of shrimp to salt solution was studied.
Isolates grown on various general and group specific growth media were identified by 16S rRNA and gyrB gene sequencing. The total microbiota and microbiological population shifts of shrimp under various storage conditions were examined using denaturant gradient gel electrophoresis (PCR-DGGE).
The microbiota differed somewhat during storage and among the various storage conditions; however, members of the genera Psychrobacter and Pseudoalteromonas were found to dominate the microbiota of most shrimp samples without preservative agents. Many isolates could be identified by gyrB gene sequencing as Psychrobacter immobilis or Psychrobacter cibarius and Pseudoalteromonas nigrifaciens, Pseudoalteromonas elyakovii or Pseudoalteromonas paragorgicola. Also species from the genera Planocuccus, Exiguobacterium, Carnobacterium, Pseudomonas, Chryseobacterium and Staphylococcus were detected during storage of brown shrimp. Culture-dependent and culture-independent PCR-DGGE analysis produced different results in band patterns. Both methods are therefore interesting to accurately identify the microbiota and bacterial population shifts on seafood during storage.