Microbiome dynamics, antibiotic resistance gene patterns and spoilage-associated genomic potential in fresh anchovies stored in different conditions

Giuseppina Sequino; Vincenzo Valentino; Alessia Esposito; Stefania Volpe; Elena Torrieri; Francesca De Filippis; Danilo Ercolini

doi:10.1016/j.foodres.2023.113788

Microbiome dynamics, antibiotic resistance gene patterns and spoilage-associated genomic potential in fresh anchovies stored in different conditions

Food Res Int. 2024 Jan:175:113788. doi: 10.1016/j.foodres.2023.113788. Epub 2023 Dec 3.

Authors

Giuseppina Sequino¹, Vincenzo Valentino¹, Alessia Esposito¹, Stefania Volpe¹, Elena Torrieri¹, Francesca De Filippis², Danilo Ercolini³

Affiliations

¹ Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici, Italy.
² Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici, Italy; Task Force on Microbiome Studies, University of Naples Federico II, Corso Umberto I 40, 80138 Naples, Italy. Electronic address: francesca.defilippis@unina.it.
³ Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici, Italy; Task Force on Microbiome Studies, University of Naples Federico II, Corso Umberto I 40, 80138 Naples, Italy.

PMID: 38129066
DOI: 10.1016/j.foodres.2023.113788

Abstract

Fresh fish is a highly perishable product and is easily spoiled by microbiological activity and chemical oxidation of lipids. However, microbial spoilage is the main factor linked with the rapid fish sensorial degradation due to the action of specific spoilage organisms (SSOs) that have the ability to dominate over other microorganisms and produce metabolites responsible for off-flavours. We explored the microbial dynamics in fresh anchovies stored in different packaging (air, modified atmosphere, under vacuum) and temperatures (0, 4 and 10 °C) using shotgun metagenomics, highlighting the selection of different microbial species according to the packaging type. Indeed, Pseudoalteromonas nigrifaciens, Psychrobacter cryohalolentis and Ps. immobilis, Pseudomonas deceptionensis and Vibrio splendidus have been identified as the main SSOs in aerobically stored anchovies, while Shewanella baltica, Photobacterium iliopiscarium, Ps. cryohalolentis and Ps. immobilis prevailed in VP and MAP. In addition, we identified the presence of spoilage-associated genes, leading to the potential production of biogenic amines and different off-flavors (H₂S, TMA). In particular, the abundance of microbial genes leading to BA biosynthesis increased at higher storage temperature, while those related to H₂S and TMA production were enriched in aerobically and VP packed anchovies, suggesting that MAP could be an effective strategy in delaying the production of these compounds. Finally, we provided evidence of the presence of a wide range of antibiotic resistance genes conferring resistance to different classes of antibiotic (β-lactams, tetracyclines, polymyxins, trimethoprims and phenicols) and highlighted that storage at higher temperature (4 and 10 °C) boosted the abundance of ARG-carrying taxa, especially in aerobically and MAP packed fish.

Keywords: Antibiotic-resistance genes; Fish microbiome; Fish off-flavours; Fish packaging; Food metagenomes; Food spoilage.

MeSH terms

Animals
Anti-Bacterial Agents / pharmacology
Food Microbiology
Food Packaging*
Food Preservation
Genomics
Microbiota* / genetics

Substances

Anti-Bacterial Agents