Importance of Microbiome in the Food industry
NGS vs “Golden standards”
In recent years there has been an explosion of next generation sequencing (NGS) techniques. NGS techniques have high-throughputs and produce thousands or even millions of sequences at the same time. These sequences allow for the accurate identification of microbial taxa, including uncultivable organisms and those present in small numbers. NGS techniques have revolutionized the field of microbial ecology and have recently been employed in the study of several food ecosystems, with promising perspectives.
The most important findings include those made in the study of the microbiota of milk, fermented dairy products, and plant-, meat- and fish-derived fermented foods. The knowledge that can be gained on microbial diversity, population structure and dynamics via the use of NGS could be vital in improving the monitoring, manipulation and food safety.
Foods harbor complex microbial communities composed of viruses, bacteria and fungi. Some of these microorganisms are of technological importance and invest foods with desirable sensorial (organoleptic and rheological) characteristics. However, undesirable microorganisms may also be present; these can reduce the quality of foods (spoilage microorganisms) or even negatively affect their safety (pathogens).
The traditional way of determining the composition of food-associated microbiotas relay on the isolation and cultivation of microorganisms prior to their identification and typing. However, it has been repeatedly shown that culturing is unreliable for the complete microbial characterization of many ecosystems, including those of foods. The selective isolation of microorganisms may require unknown growth factors and/or growth conditions present in natural habitats that are not reproduced by laboratory media. Foods may also have a low pH, a reduced aw, or have to be kept under harsh storage conditions, etc., which might leave microbes in a physiologically viable but not cultivable state. Moreover, microbes present in low numbers can be outcompeted by numerically more abundant species, impeding their detection in culture. Such limitations lead these techniques to underestimate microbial diversity, and sometimes even the failure to detect the majority microbial groups.
Benefits of Monitoring
Conventional microbial testing is limited in its ability to lead food safety and quality professionals to the source of problems, as it does not provide sufficient information for systematic monitoring and therefore does not offer the possibility of predicting negative consequences. This limits the industry to a reactive position to manage and control problems from pathogens and spoilage organisms.
Storage conditions, packaging, pH, temperature, and water activity can influence food quality and shelf life among other factors. Shelf-life estimates, however, have traditionally been based on rudimentary statistical models incapable of accounting for the complexity of factors that impact food freshness, more specifically not being able to take into consideration the composition and quantity of all microbial communities present on any food sample. These limitations have long been recognized by food scientists and have led them to look for cost-effective alternatives.
Looking ahead, we expect that multi-use, and hyper-efficient tools with reduced physical footprints will gain market share. NGS is a great example of this, as it allows any lab to gather millions of data about a single sample. It moves beyond the binary yes-no response of traditional testing, and lets you get much more done, with far less. Such wealth of information not only increases the confidence about the result, but can also be mined to generate more actionable insights for interventions and root cause analysis.
This is very in-line with the “Smarter Tools and Approaches” that FDA described in their new approach to food safety.
Over time, as individual manufacturers and the industry as a whole analyze more and more samples and generate more data, we should be able to develop increasingly accurate predictive models. The data generation cost and logistics could be significantly streamlined if existing food safety tests evolve to broader vehicles that can create insights on both safety and quality indications of food product simultaneously. By comparing the observed (or expected) microbiome profile of a fresh product with the models we develop, we could greatly improve our estimates of a given product’s remaining shelf life.
Authenticity & Traceability of raw materials
Identification of the species present in food and feed samples is a critical step for proof of authenticity, traceability of raw materials, and quality control of handling and cleaning processes in food production lines. Screening of food samples against an extensive database of meat, fish and plant species, including exotic variants, gives accurate detection and differentiation of expected and unexpected species.
• Better supply chain control
• Improved product quality assurance
• Higher levels of confidence
• Reduced risk of recalls and notifications
• Increased brand protection and consumer trust
Benefits of an untargeted screening approach
NGS untargeted approach enables accurate detection and differentiation of thousands of different species in each sample using DNA sequencing. At the end of an NGS analysis, millions of individual sequences are obtained making it possible to identify species in complex foods containing multiple ingredients, as they are compared against a database resulting in a complete list of all the species present in the sample.
There is no requirement for previous knowledge of the supply chain, or which targets to search for. This means that now the question can be simply; “which meat species are in my sausage meat?”, or “are there any other plants in my dried oregano”, and “can I defend my label claims?”