Mycotoxins are toxic substances that can infect many foods with carcinogenic, genotoxic, teratogenic, nephrotoxic, and hepatotoxic effects. Mycotoxin contamination of foodstuffs causes diseases worldwide. The major classes of mycotoxins that are of the greatest agroeconomic importance are aflatoxins, ochratoxins, fumonisins, trichothecenes, emerging Fusarium mycotoxins, enniatins, ergot alkaloids, Alternaria toxins, and patulin. Thus, in order to mitigate mycotoxin contamination of foods, many control approaches are used. Prevention, detoxification, and decontamination of mycotoxins can contribute in this purpose in the pre-harvest and post-harvest stages. Therefore, the purpose of the review is to elaborate on the recent advances regarding the occurrence of main mycotoxins in many types of important agricultural products, as well as the methods of inactivation and detoxification of foods from mycotoxins in order to reduce or fully eliminate them.

Fermented foods identify cultures and civilizations. History, climate and the particulars of local production of raw materials have urged humanity to exploit various pathways of fermentation to produce a wide variety of traditional edible products which represent adaptations to specific conditions. Nowadays, industrial-scale production has flooded the markets with ferments. According to recent estimates, the current size of the global market of fermented foods is in the vicinity of USD 30 billion, with increasing trends. Modern challenges include tailor-made fermented foods for people with special dietary needs, such as patients suffering from Crohn’s disease or other ailments. Another major challenge concerns the safety of artisan fermented products, an issue that could be tackled with the aid of molecular biology and concerns not only the presence of pathogens but also the foodborne microbial resistance. The basis of all these is, of course, the microbiome, an aggregation of different species of bacteria and yeasts that thrives on the carbohydrates of the raw materials. In this review, the microbiology of fermented foods is discussed with a special reference to groups of products and to specific products indicative of the diversity that a fermentation process can take. Their impact is also discussed with emphasis on health and oral health status. From Hippocrates until modern approaches to disease therapy, diet was thought to be of the most important factors for health stability of the human natural microbiome. After all, to quote Pasteur, “Gentlemen, the microbes will have the last word for human health.” In that sense, it is the microbiomes of fermented foods that will acquire a leading role in future nutrition and therapeutics.

Nowadays, food treatment technologies are constantly evolving due to an increasing demand for healthier and tastier food with longer shelf lives. In this review, our aim is to highlight the advantages and disadvantages of some of the most exploited industrial techniques for food processing and microorganism deactivation, dividing them into those that exploit high temperatures (pasteurization, sterilization, aseptic packaging) and those that operate thanks to their inherent chemical–physical principles (ultrasound, ultraviolet radiation, ozonation, high hydrostatic pressure). The traditional thermal methods can reduce the number of pathogenic microorganisms to safe levels, but non-thermal technologies can also reduce or remove the adverse effects that occur using high temperatures. In the case of ultrasound, which inactivates pathogens, recent advances in food treatment are reported. Throughout the text, novel discoveries of the last decade are presented, and non-thermal methods have been demonstrated to be more attractive for processing a huge variety of foods. Preserving the quality and nutritional values of the product itself and at the same time reducing bacteria and extending shelf life are the primary targets of conscious producers, and with non-thermal technologies, they are increasingly possible.

Eating fresh fruits and vegetables is, undoubtedly, a healthy habit that should be adopted by everyone (particularly due to the nutrients and functional properties of fruits and vegetables). However, at the same time, due to their production in the external environment, there is an increased risk of their being infected with various pathogenic microorganisms, some of which cause serious foodborne illnesses. In order to preserve and distribute safe, raw, and minimally processed fruits and vegetables, many strategies have been proposed, including bioprotection. The use of lactic acid bacteria in raw and minimally processed fruits and vegetables helps to better maintain their quality by extending their shelf life, causing a significant reduction and inhibition of the action of important foodborne pathogens. The antibacterial effect of lactic acid bacteria is attributed to its ability to produce antimicrobial compounds, including bacteriocins, with strong competitive action against many microorganisms. The use of bacteriocins, both separately and in combination with edible coatings, is considered a very promising approach for microbiological quality, and safety for postharvest storage of raw and minimally processed fruits and vegetables. Therefore, the purpose of the review is to discuss the biopreservation of fresh fruits and vegetables through the use of lactic acid bacteria as a green and safe technique.

The accomplishment of food/nutrition security for all across sustainable food systems (SFS) is tied to the Sustainable Development Goals (SDGs). SFS is connected to all SDGs via the traditional framework of social inclusion, economic development, environmental safety, inclusivity, and the development of sustainable food systems. We suggest that, for the world to achieve sustainable development, a shift to SFS is necessary to guarantee food/nutrition security for all, while operating within planetary boundaries to protect ecosystems and adapt to and mitigate climate change. Therefore, there is a requirement for original approaches that implement systemic and more participatory methods to engage with a wider range of food system stakeholders. However, the lack of skills and tools regarding novel methodologies for food system transformation is a key obstacle to the deployment of such approaches in practice. In the first part of this review, a summary of some challenges that occur in the governance of food system transformation is given. Through a case study of plant-based proteins and their biological and chemical modification as diets shift towards alternative proteins, we demonstrate that resource-efficient food systems and food waste, through system transformation, are useful in understanding both (i) how food system transformation has ensued and (ii) how the required transformation is prohibited. Finally, we discuss the implications of food system transformation in terms of nutrition and sustainable healthy diets, which are needed to achieve changes in food safety systems in the future. The linkage of food and the environment is evident, focusing on nutrition and sustainable healthy diets. This cannot be accomplished without system change and research towards new foods and, more specifically, new proteins such as plant-based ones and their biological and chemical modification.