Contribution of data acquired from spectroscopic, genomic and microbiological analyses to enhance mussels’ quality assessment

Date published

2024-12-01

Free to read from

2025-02-26

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Journal Title

Journal ISSN

Volume Title

Publisher

Elsevier

Department

Type

Article

ISSN

0963-9969

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Citation

Lytou A, Saxton L, Fengou L-C, et al., (2024) Contribution of data acquired from spectroscopic, genomic and microbiological analyses to enhance mussels’ quality assessment. Food Research International, Volume 197, Issue Pt 1, December 2024, Article number 115207

Abstract

In this study, a large amount of heterogeneous data (i.e., microbiological, spectral and Next Generation Sequencing data) were obtained analyzing mussels of different species and origin, to acquire a comprehensive view about the quality and safety of these products. More specifically, spectral data were collected through Fourier transform Infrared (FTIR) spectroscopy, while the overall profile of microorganisms present in these samples, affecting quality and safety of mussels throughout storage, was determined through Next Generation Sequencing (NGS) using 16S rRNA metabarcoding analysis. In parallel, conventional microbiological analysis for the estimation of culturable spoilage microorganisms (total aerobes, Pseudomonas spp., B. thermosphacta, Shewanella spp. and Enterobacteriaceae) was applied. Different machine learning algorithms, namely Partial Least Square (PLS), Support Vector Machines (SVM), k-Nearest Neighbors (kNN), Random Forest (RF) Neural Networks (NN)) were applied accordingly, to assess the potential of FTIR and NGS data to provide useful information about mussels’ microbiological quality. Microbial counts ranged from 3.5 to 9.0 log CFU/g, while NGS revealed several bacterial genera such as Pseudoalteromonas, Psychrobacter, Acinetobacter, Pseudomonas, B. thermosphacta, Psychrobacter, Kistimonas, Psychrilyobacter to affect the quality of mussels, depending on the mussel species, batch and storage conditions. According to the performance metrics, the SVM algorithm in tandem with FTIR achieved the highest prediction accuracy for microbial counts in M. chilensis samples (Rsquared; 0.89, RMSE; 0,74), while in the case of predicting the abundance of microbial genera using spectroscopic data, the best performing algorithm varied by bacterial genus. Indicatively, in M. chilensis, RF, kNN and NN performed better in predicting Enterococcus, Enhydrobacterium and Pseudoalteromonas, respectively (Rsquared = 0.92, 0.93, 0.99). Associations between genomics data and specific spectral regions were further investigated, revealing certain spectral regions that are associated with mussels’ quality and safety. The application of “multi-omics” in seafood supply chain can provide insightful information about mussels’ quality and safety compared to the methodologies followed in current quality and safety management systems.

Description

Software Description

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Github

Keywords

Next generation sequencing, FTIR, Spoilage, Multi-omics, Seafood, Machine learning, 30 Agricultural, Veterinary and Food Sciences, 32 Biomedical and Clinical Sciences, 40 Engineering, 4004 Chemical Engineering, 3210 Nutrition and Dietetics, 3006 Food Sciences, Machine Learning and Artificial Intelligence, Biotechnology, FTIR, Machine learning, Multi-omics, Next generation sequencing, Seafood, Spoilage, Food Science, 3006 Food sciences, 3210 Nutrition and dietetics, 4004 Chemical engineering

DOI

Rights

Attribution 4.0 International

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Funder/s

European Commission