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Tracing seafood at high spatial resolution using NGS-generated data and machine learning: Comparing microbiome versus

Massimo Milan1, Francesco Maroso2, Giulia Dalla Rovere3

  • 1Department of Comparative Biomedicine and Food Science, University of Padova, 35020 Legnaro, Italy; CONISMA - Consorzio Nazionale Interuniversitario per le Scienze del Mare, Roma, Italy.

Food Chemistry
|March 5, 2019
PubMed
Summary

Next-generation sequencing (NGS) of microbiome data accurately traces the geographic origin of Manila clams. This cost-effective method offers high-resolution seafood traceability, outperforming genetic analysis.

Keywords:
Food traceabilityMachine learningManila clam Ruditapes philippinarumMicrobiomeNGSShellfishVenice lagoon

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Area of Science:

  • Marine Biology
  • Genomics
  • Food Science

Background:

  • Food traceability is crucial for producers and regulators.
  • Ensuring the origin of commercially important seafood like Manila clams is challenging.
  • Next-generation sequencing (NGS) offers potential for novel traceability solutions.

Purpose of the Study:

  • To evaluate the efficacy of NGS-generated data for seafood traceability.
  • To compare the accuracy of microbiome data versus single nucleotide polymorphisms (SNPs) for determining clam origin.
  • To develop a high-resolution method for tracing the geographic origin of Manila clams.

Main Methods:

  • Collected Manila clams (Ruditapes philippinarum) from authorized and contaminated harvesting areas in the Venice lagoon.
  • Analyzed both microbiome composition and single nucleotide polymorphisms (SNPs) from clam samples.
  • Applied machine-learning techniques to microbiome data for origin determination.

Main Results:

  • Microbiome data provided more accurate geographic origin determination for Manila clams than SNP data.
  • Combining microbiome data with machine learning enabled high-resolution tracing of clam origin.
  • NGS analysis of microbiome data proved to be a cost-effective and portable solution.

Conclusions:

  • NGS-based microbiome analysis is a reliable and high-resolution tool for seafood traceability.
  • This approach can accurately pinpoint the origin of Manila clams.
  • The method offers a cost-effective alternative for food origin verification.