Research project
36 | monthsSERFIN

Assessment of new and re-emerging biological risks in traditional and novel food chains of animal origin

Related toSpoke 03
Principal investigators
Angela Di Pinto
Other partecipantsAnna Mottola

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Highlights

Project partners

Università degli Studi di Bari Aldo Moro

Coordinator

Work packages involved

WP 3.1

Assessment of new and re-emerging risks in the food system

WP leader

Università degli Studi di Bari Aldo Moro

Task involved

Task 3.1.1.

Standard protocols (ISO), whole genome sequencing (WGS), computational methodologies, and MetaOmic approaches (metagenomics, metatrascriptomics, metabolomics, lipidomics, culturomics and phenomics) will be applied for the identification and characterization of the new and (re)-emerging chemical and biological hazards in traditional products, related to climate changes, microbial evolution, and modifications in the manufacturing processes. Omics techniques will also be applied to study factors affecting the survival and the stress resistance mechanisms of pathogens and antimicrobial resistant (AMR) bacteria during food processing and shelf life. In addition, a CAD-based automatic feature recognition procedure will be developed for hygienic design of food machinery, as a prerequisite for GMP in food production.

Project deliverables

D3.1.1.1.

Database of WGS data of foodborne pathogens (M24)

D3.1.1.2.

Omics protocols to evaluate food safety

D3.1.1.4.

Identification of AMR risk factors in food products

State of the art

Advanced analysis tools can help to fully characterize these products and assess new and re-emerging risks in the food system. Recently, several studies have shown that High-Throughput DNA Sequencing (HTS) is a powerful approach in food safety programs providing details of the species composition and the microbial signature, thus enabling its geographical origin and/or hygienic and sanitary conditions to be traced (Frigerio et al., 2020).

Operation plan

The research will apply DNA metabarcoding to characterize traditional and novel food matrices. After DNA extraction, species composition will be verified through the metabarcoding of the mitochondrial Cytochrome Oxidase I (COI) gene region. 

Furthermore, the microbial safety of products will be assessed by metabarcoding of three molecular markers: 

  • the 16S ribosomal RNA (rRNA) gene to characterize prokaryotic communities; 
  • the 18S ribosomal RNA (rRNA) gene to survey microeukaryotes;  
  • RNA-dependent RNA polymerases (RdRPs) to detect RNA viruses; 
  • and  the Internal Transcribed Spacer (ITS) to assess fungi communities. 

Metabarcode fragments will be sequenced using second- and/or third-generation sequencing technologies. Bioinformatics analysis will be performed to generate specific profiles for each molecular marker.

Expected results

For each type of food matrix, the results obtained from the selected markers will be integrated to provide full product profiles.

  • In terms of species composition, it will be possible to evaluate the purity of the product or the presence of unexpected animal taxa that could occur randomly or regularly in the different types of products.
  • The full microbial fingerprint (bacteria, viruses, protists, and fungi) will be obtained in order to evaluate the safety of the products, and to provide data to implement safety standards in the food processing industry, in addition to getting information about the sanitary conditions in the specific food supply chain. This will also help to highlight the presence of randomly- or regularly-occurring pathogens and parasites.