Evolution of the indigenous microbiota in modified atmosphere packaged Atlantic horse mackerel (Trachurus trachurus) identified by conventional and molecular methods

A combination of conventional methods and genetic identification (PCR sequencing) was used to study the dynamics of the bacterial population during the spoilage of modified atmosphere packaged (MAP) Atlantic horse mackerel (Trachurus trachurus) fillets. The cultivable microflora in Atlantic horse mackerel samples packaged in a modified atmosphere (48% CO2, 50% N2 and 2% O2) at refrigeration temperature (6 °C) was measured on days 1, 5 and 7 using non-selective (Long and Hammer agar) and selective media (Kliglerʹs iron agar, STAA and MRS). The microflora was genetically characterised using partial amplification of 16S rRNA gene sequences from 309 bacterial isolates obtained from Long and Hammer agar. At the end of the shelf life (5 days), the total viable counts (TVC) on Long and Hammer agar were not significantly different to the LAB counts on MRS agar (p > 0.05). The molecular approach showed that Photobacterium, Arthrobacter, Chryseobacterium and Pseudoclavibacter (44.5% of total) dominated the microbial composition of the fish at the beginning of storage. However, Serratia, Shewanella and Yersinia dominated at the late spoilage stages (over 57.2% of the total). Carnobacterium was the most important species of the lactic acid bacteria (LAB) and was identified at the beginning and end of the storage period. Vibrio spp. was only found at the end of the shelf life. This research demonstrates that the microbial biodiversity in MAP Atlantic horse mackerel is enormous and the dominant species change over the storage time. The results presented here on the dominant communities in fish products will make it possible to accurately select the best preservation practices.