DNA based methodologies have proved to be sensitive, accurate and easy-to-use tools to address the problem of food adulteration or quality/safety. DNA metabarcoding, among many DNA methodologies, is regarded as a suitable tool to describe the composition of processed food. This methodology can be used to detect food adulteration (intentional addition and substitution of food ingredients) or the contamination by substances that are added to food products unintentionally along the production process. This thesis centred around testing the application of DNA metabarcoding in a case study on ready-to-eat processed meat products collected in South Africa (SA). To date, these meat products represent the primary source of protein intake in SA’s lower-income sectors, mainly due to their affordability.
Since the use of DNA metabarcoding in food control is still a tool in development, the first chapter presents the result of a pilot study which compared three DNA extraction methods for extraction of DNA in eight ready-to-eat processed meat products. We evinced a cost-efficient and time-effective approach for extraction of DNA, suitable for downstream qualitative species analysis with metabarcoding, on highly processed meat samples. In this chapter, we also provide guidelines for establishing an effective DNA metabarcoding workflow for large-scale testing of processed food products.
In the second chapter, the DNA metabarcoding workflow optimised in Chapter 1 was used to test the authenticity (i.e. presence of adulterants) of processed meat products (233 in total). The detection of food adulterants is a significant concern not only from an economic point of view, but also in relation to food allergies, medical requirements, religious practices, and ethical reasons. We detected a significantly high rate, 49.3%, of substitution due to the presence of different animal adulterants. The undeclared animal species were generally domestic species (cattle, chicken, pig, goat and donkey). Unconventional species for the type of meat product under analysis were discovered in some products: Burchell's zebra, antelopes (blue wildebeest, gemsbok, hartebeest, red hartebeest and common eland) and kangaroo species (eastern grey kangaroo, red kangaroo and wallaby). In this chapter, we also describe the plant composition of ready-to-eat processed meat products.
In the last chapter, the presence of spoilage and foodborne microorganisms, as a result of contamination during the production, was investigated by using DNA metabarcoding in the same set of samples examined for authenticity. The contamination by foodborne poisoning agents in food is a widespread major health problem and frequently of paramount medical importance. The presence of spoilage-causing microorganisms in food is the dominant contributing factor of global food wastage. The study describes the microbiota of processed meat. Our study confirms the importance of the use of quality ingredients and appropriate hygienic measures in the processing environment. We present the evidence that both the animal ingredients may explain the presence and/or the higher load of certain bacterial species and that foods from different production facilities have significantly different microbiome compositions.
Overall, our study supports the use of DNA metabarcoding for the authentication of processed food products and for large-scale food quality monitoring.