Abstract
This work aimed to identify the key members of the bacterial community growing on common carp (Cyprinus carpio) fillets during chilled storage with next-generation sequencing (NGS) and cultivation-dependent methods. Carp fillets were stored for 96 h at 2 °C and 6 °C with and without a vacuum package, and an additional frozen-thawed storage experiment was set for 120 days. Community profiles of the initial and stored fish samples were determined by amplicon sequencing. Conventional microbial methods were used parallelly for the enumeration and cultivation of the dominant members of the microbial community. Cultivated bacteria were identified with 16S rRNA sequencing and the MALDI-TOF MS method. Based on our results, the vacuum package greatly affected the diversity and composition of the forming microbial community, while temperature influenced the cell counts and consequently the microbiological criteria for shelf-life of the examined raw fish product. Next-generation sequencing revealed novel members of the chilled flesh microbiota such as Vagococcus vulneris or Rouxiella chamberiensis in the vacuum-packed samples. With traditional cultivation, 161 bacterial strains were isolated and identified at the species level, but the identified bacteria overlapped with only 45% of the dominant operational taxonomic units (OTUs) revealed by NGS. Next-generation sequencing is a promising and highly reliable tool recommended to reach a higher resolution of the forming microbial community of stored fish products. Knowledge of the initial microbial community of the flesh enables further optimization and development of processing and storage technology.
Highlights
Common carp is an extremely perishable food (Li et al 2017a); spoilage occurs rapidly leading to a limited shelflife for carp products (Gram and Huss 1996)
At the time of sampling, water samples were dominated by hydrogen-carbonate, while sediment samples had a higher concentration of sulphate (400–800 mg/ kg dry mass) and calcium ions (340–511 mg/kg dry mass)
This paper aims to improve the understanding and knowledge of the storage microbiota of carp fillet originated from a European polyculture with low population density
Summary
Common carp is an extremely perishable food (Li et al 2017a); spoilage occurs rapidly leading to a limited shelflife for carp products (Gram and Huss 1996). The initial bacterial community of stored carp is mainly composed of psychrotrophic Gram-negative bacteria from the genera Pseudomonas, Moraxella, Acinetobacter, Shewanella, and Flavobacterium (Gram and Huss 1996) Depending on their spoilage potential, some of these organisms may contribute to the quality changes of fish (Beaz-Hidalgo et al 2014). To identify the species of bacteria from samples, traditional cultivation methods, often merged with 16S rRNA gene sequencing, have been utilized previously (Zhang et al 2015; Wang et al 2017) Based on these findings, a total of 13 different genera comprised the microbial communities of fresh common carp fillets with the dominance of Acinetobacter species. During storage of VP carp fillets, H 2S producing bacteria and especially lactic acid bacteria (LAB) counts increased slightly towards the end of the shelf life (Zhang et al 2015)
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