Unveiling hákarl: A study of the microbiota of the traditional Icelandic fermented fish

• Published in: Food Microbiology
• Main Authors: Andrea Osimani, Ilario Ferrocino, Monica Agnolucci, Luca Cocolin, Manuela Giovannetti, Caterina Cristani, Michela Palla, Vesna Milanovic, Andrea Roncolini, Riccardo Sabbatini, Cristiana Garofalo, Francesca Clementi, Federica Cardinali, Annalisa Petruzzelli, Claudia Gabucci, Franco Tonucci, Lucia Aquilanti
• Other Authors: Osimani, Andrea, Ferrocino, Ilario, Agnolucci, Monica, Cocolin, Luca, Giovannetti, Manuela, Cristani, Caterina, Palla, Michela, Milanovic, Vesna, Roncolini, Andrea, Sabbatini, Riccardo, Garofalo, Cristiana, Clementi, Francesca, Cardinali, Federica, Petruzzelli, Annalisa, Gabucci, Claudia, Tonucci, Franco, Aquilanti, Lucia
• Format: Article in Journal/Newspaper
• Language: English
• Published: 2019
• Subjects: Tissierella; Pseudomona; Debaryomyce; 16S amplicon-based sequencing; PCR-DGGE; Greenland; Somniosus microcephalus
• Online Access: http://hdl.handle.net/11568/987329; https://doi.org/10.1016/j.fm.2019.03.027

Hákarl is produced by curing of the Greenland shark (Somniosus microcephalus) flesh, which before fermentation is toxic due to the high content of trimethylamine (TMA) or trimethylamine N-oxide (TMAO). Despite its long history of consumption, little knowledge is available on the microbial consortia involved in the fermentation of this fish. In the present study, a polyphasic approach based on both culturing and DNA-based techniques was adopted to gain insight into the microbial species present in ready-to-eat hákarl. To this aim, samples of ready-to-eat hákarl were subjected to viable counting on different selective growth media. The DNA directly extracted from the samples was further subjected to Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) and 16S amplicon-based sequencing. Moreover, the presence of Shiga toxin-producing Escherichia coli (STEC) and Pseudomonas aeruginosa was assessed via qualitative real-time PCR assays. pH values measured in the analyzed samples ranged from between 8.07 ± 0.06 and 8.76 ± 0.00. Viable counts revealed the presence of total mesophilic aerobes, lactic acid bacteria and Pseudomonadaceae. Regarding bacteria, PCR-DGGE analysis highlighted the dominance of close relatives of Tissierella creatinophila. For amplicon sequencing, the main operational taxonomic units (OTUs) shared among the data set were Tissierella, Pseudomonas, Oceanobacillus, Abyssivirga and Lactococcus. The presence of Pseudomonas in the analyzed samples supports the hypothesis of a possible role of this microorganism on the detoxification of shark meat from TMAO or TMA during fermentation. Several minor OTUs (<1%) were also detected, including Alkalibacterium, Staphylococcus, Proteiniclasticum, Acinetobacter, Erysipelothrix, Anaerobacillus, Ochrobactrum, Listeria and Photobacterium. Analysis of the yeast and filamentous fungi community composition by PCR-DGGE revealed the presence of close relatives of Candida tropicalis, C. glabrata, C. parapsilosis, C. zeylanoides, ...