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

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.