From DNA sequencing and metagenomics to mycotoxins and GMOs at RME

FoodQualityNews was a media partner at the conference which focussed on microbiological and chemical analysis of food, feed and water.

Rachel Glover​ of Fera said microbial ecology methods (metabarcoding) can profile all species in a food sample unique to the environment it was prepared in whereas DNA barcoding looks at one thing.

She said they were looking at the Oxford Nanopore MinION device and cited work from the University of Nottingham​ on a novel technique for selective DNA sequencing, called ‘Read Until’.

Glover added ongoing work includes looking at oysters to see if they come from where they claim and fungal and bacterial metabarcoding of stilton cheese to find where it is produced.

Fera Science previously told us about a service using Whole Genome Sequencing (WGS) to identify the source and trace the route of bacterial contamination called OriGen​.

REIMS, MALDI-TOF and metagenomics​

Sara Stead of Waters Corporation said Rapid evaporative ionisation MS (REIMS) can be used for characterisation of water containing food.

Proof of principle applications have been developed for detection of undeclared ingredients in processed foods and product authenticity such as Mortadella di Bologna (an Italian sausage) or geographical origin of pistachio nuts and botanical origin of monofloral honey.

She said mass spectrometry methods have been considered to be slow and expensive with extensive sample preparation procedures but ambient ionisation MS (AIMS) improved this situation.

Waters is looking at microorganisms with Imperial College London and at automation with Tecan’s Pickolo colony-picker and Freedom EVO platform.

The firm acquired REIMS from MediMass a company created by Imperial’s Professor Zoltan Takats.

Annegret Manning​, of Chemisches und Veterinäruntersuchungsamt Stuttgart (CVUAS), said it is looking at matrix assisted laser desorption/ionisation time of flight mass spectrometry (MALDI-TOF MS) from Bruker.

It is building a database​ with more than 50 data entries of different animal species (beef, pork, chicken) as no commercial one exists for identification of animal species.

Luca Cocolin​, from the University of Torino, said it was important to use correct terminology when referring to new methods.

Studying the microbial ecology of foods can use approaches based on next generation sequencing (NGS) such as metagenetics (or 16S rRNA metagenomics) and metagenomics.

Cocolin said the information from these methodologies is ‘very different’ and must be taken into account to avoid misinterpretation of the data.

Metagenetics is a PCR-based methodology which can reveal the ecology of an ecosystem based on the primers used for amplification.

Metagenomics reaches the ecological description by isolating sequences belonging to the rRNA genes and catalogues the genes present in the microbial ecosystem.

Karsten Haupt​, from Sorbonne University, presented on molecularly imprinted polymers (MIPs) which are synthetic antibody mimics that recognise molecular targets.

The functional nanomaterials could be used in sample preparation, immunoassays and biosensors.

Miguel Angel Pardo​, from AZTI-Tecnalia, presented on recombinase polymerase amplification (RPA) to control integrity of food products.

He said PCR requires precise temperature control and rapid thermocycling steps at dissociation (95 degrees Celsius), annealing (55-65) and elongation (70).

Three isothermal amplifications have been described: LAMP, nicking enzyme amplification reaction (NEAR) and helicase-dependant amplification (HDA) but HDA and NEAR require an initial denaturation step at 95 degrees and LAMP needs complex primer designs.

RPA helps the binding of oligonucleotide primers to template DNA, said Angel Pardo.

It is suitable to discriminate food ingredients within 15 minutes excluding DNA isolation, he added.

EU project work​

Esther Kok​ from RIKILT Wageningen University and Research, said polymerase chain reaction (PCR) is still the gold standard sometimes complemented by DNA sequencing.

Amplification strategies such as loop-mediated isothermal amplification (LAMP) or digital (droplet) PCR and sequencing like single molecule and restriction site-associated (RAD) sequencing with related bioinformatics tools are some methods.

Presenting work on the DECATHALON EU project, she said methods are becoming more diverse, from hand-held and point of use devices to lab-based screening strategies.

Marko Bohane​c, of the Jozef Stefan Institute, talked about the development of SIGMO​ (System for Identification of GM Organisms).

It assesses the likelihood that a food product contains authorised or unauthorised GM materials based on traceability and analytical data about the product.

The software was developed as part of the DECATHALON project so work is ongoing to extend it as a stand-alone and how to maintain it as the project has ended.

MycoKey will deliver an ICT tool to address mycotoxin contamination along the food and feed chain by 2019.

The EU project is holding a conference, with the MyToolBox consortium, on reduction of mycotoxin in Ghent, Belgium 11-14 September.

MycoKey​,​ funded by European Commission under Horizon 2020 programme, has 32 partners from Europe, China, Nigeria and Argentina.

MyToolBoxinvolves 23 partners from 11 countries and is co-ordinated by the University of Natural Resources and Life Sciences (BOKU) in Vienna.

Diego L. Garcia-Gonzalez,​ from the Instituto de la Grasa of CSIC, explained how Fourier Transform mid infrared spectroscopy (FTIR) with attenuated total reflectance (ATR) was applied to characterise vinegars in the FoodIntegrity project.

He said vinegar is considered as a high quality product with some registered as Protected Designation of Origin (PDO).

Peter Cockburn​ of the Scotch Whisky Research Institute also presented work as part of the same EU project.

SpiritsEurope, another partner in the project, said according to estimates, the market share of counterfeit European products is around 25% of all imported spirits sold in China.

In Bulgaria, illicit spirits are believed to make up more than 50% of domestic spirit consumption, added the association.

Cockburn said there is Generic Authenticity – trading on the quality associated with a category of spirit drink and Brand Authenticity – trading on the quality from a brand of spirit drink.

He added not one tool fits all with GC-FID, HPLC-UV, GC-MS and IC with PAD among techniques used.

Ocean Optics’ UV-VIS spectrometer, Rida Cube from R-Biopharm, Snap 50 from Anton Paar and Torion T-9 GC-MS from PerkinElmer are examples of other systems used.