Characterisation of the microbiota of Atlantic mackerel (Scomber scombrus)

In this study the microbiota of Atlantic mackerel (Scomber scombrus) collected by a commercial purse seiner was examined. Fish were collected directly from the purse seine and from the Refrigerated Sea Water (RSW) transport tank after loading. The culturable microbiota and Specific Spoilage Bacteria (SSB) were quantified on Iron Agar Lyngby (IAL) and identified using commercially available Biochemical API® kits on pure cultured isolates. These kits showed to be sub-optimal in characterising the isolates, since only half of the strains were identified. The same isolates were also identified by a nucleic acid based PCR-DGGE approach, and only half of the sequences gave the same results as the API®. Characterisation by PCR-DGGE was also performed on bacterial DNA from IAL plates (bulk cell samples) and on samples where the bacterial DNA was extracted directly from fish material without any cultivation (direct DNA samples). The microbiota of Atlantic mackerel was dominated by members of the Gram-negative genera as Psychrobacter sp., Proteus sp., Photobacterium sp., Vibrio sp., Shewanella sp., Synechococcus sp., Oceanisphaerae sp., Bizonia sp., Pseudoalteromonas sp., and members of Flavobacteriaceae. Gram-positive bacteria in the genera Vagococcus sp., Bacillus sp., Mycobacterium sp., Staphylococcus sp., Mycoplasma sp. and Clostridia sp. were also found. Examination by PCR-DGGE and sequencing of the bulk cell pellet after cultivation on IAL, gave a higher number of taxa as compared to extraction and examination of bacterial DNA from fish materials without prior cultivation. This shows the benefit of combining both culture dependent and culture independent methods, when studying the microbiota of marine fish. Several Vibrio spp. were found only in gut samples collected from the purse seine, but in all samples including the skin and the gills collected from the RSW tank, indicating microbial contamination by faecal bacteria from the fish under these transport conditions.

► We apply conventional and DNA based methods to describe microbiota of mackerel.
► Skin, gills and intestinal contents of commercially caught mackerel were examined.
► This combination of methods enhances the description of microbiota.
► Test kits (API) are not optimal in identification of isolates from marine fish.
► Pumping of fish decreases microbiological quality of the mackerel.