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The study of primary plant metabolism has been the main focus of scientists for several years, seconding research related to the secondary metabolism. Nowadays, with the better understanding of the processes and products involved in primary metabolism, the focus has switched to the expansion of knowledge involving secondary metabolism. Initially, plants were the focus of secondary metabolite studies due to their ease of acquisition and availability, reasons for being a term coined by plant physiologists. Only in the twentieth century has the secondary metabolites from microorganisms began to be recognized and investigated due to the value that these metabolites could bring to science. Not by chance, it was in the twentieth century that the era of antibiotics began. In this chapter, a voyage through the centuries is proposed, focused on secondary metabolism and metabolites, highlighting how they shifted from disregarded molecules to the powerhouses of bioactivity for modern science.

Secondary metabolism of plants produces molecules that are widely used in the food industry for many years. The demand for these molecules has been increasing, and special focus has been given to volatile molecules. Scope: The study of secondary metabolites with special focus on the volatile molecules is overviewed, explaining their bioactivities and examples of application in the food industry. Approach: Systematic analysis of volatiles and their applications. Specific analysis of volatile components of plants and their use as active packaging and airborne food preservatives. Key findings: Some work has been done regarding volatiles in terms of food preservation but is focused mostly on postharvest protection. Considering the number of studies regarding the use of volatiles, the industry should start implementing these molecules for more sustainable approaches to preservation. Conclusions: The food industry has researched plant volatiles for some years, but the focus has been almost exclusively on postharvest protection, and more research can be directed to other food categories. Technology to overcome limitations of plant volatiles is expected to improve, placing pressure on regulatory bodies to allow these molecules in foods, on par with consumer and industry preference for natural-based molecules used in foods. The authors are grateful to the Foundation for Science and Technology (FCT, Portugal) for financial support through national funds FCT/MCTES to the CIMO (UIDB/00690/2020). Acknowledgments to the Project financed by the European Fund for Regional Development (Fundo Europeu de Desenvolvimento Regional (FEDER)) through the Programa Operacional Regional Norte 2020, within the “PlantCovid” project, NORTE-01-02B7-FEDER-054870. M. C. Pedrosa thanks “PlantCovid” project for her scholarship. S. Heleno and M. Carocho thank FCT, P.I., for their individual employment program-contract (CEECIND/00831/2018, CEECIND/03040/2017), while L. Barros thanks FCT, P.I., through the institutional scientific employment program- contract. info:eu-repo/semantics/publishedVersion

Fermented products have been gaining a notable importance in recent years due to the health benefits that they can provide in relation to the initial unfermented food matrix, i.e. in the enhancement of nutrients, effect on glucose metabolism and bioactivity, the presence of probiotics in some foods. The paper gives a current analysis of the fermented food/beverage and health relationship studies present in the literature and it is based on a literature quantitative analysis approach. VOSviewer software was utilized to extract and elaborate bibliometric data. 1504 publications ranged from the year 1970 to 2022 were retrieved by literature search and were collectively cited in 25,868 documents. The subject areas mainly covered are: “Agricultural and Biological Sciences”, “Biochemistry, Genetics and Molecular Biology”, “Immunology and Microbiology” and “Medicine”. 1148 terms, in total, are identified and the top recurring terms on the fermented food/beverage and health research are: metabolism, lactobacillus, food microbiology, lactic acid, animals. The functionality of fermented foods are here explored. Innovation is represented towards obtaining specific fermented foods (i.e. yogurts), by changing the fermentation conditions, or by adding or removing compounds that alter the fermentation, and thus, with the improvement of technologies like nanotechnology, targeted nutrition and others, it is expected that fermented food will consolidate their position in the food market. The authors are grateful to the Foundation for Science and Technology (FCT, Portugal) for financial support through national funds FCT/MCTES to the CIMO (UIDB/00690/2020). M. Carocho and S. Heleno thank FCT, for their individual employment program-contract (CEECIND/00831/2018, CEECIND/03040/2017), while L. Barros thanks FCT, through the institutional scientific employment program-contract. info:eu-repo/semantics/publishedVersion

The plant kingdom is an endless source of molecules that can be applied in almost all realms of society. The food industry has profited from the use of plants and their derived materials for many decades. Recently, the food industry has been looking into plants to find different ways of either preserving, coloring or sweetening foods. In this work, leaf extracts of Arbutus unedo L. obtained by dynamic maceration and ultrasound assisted extraction with prior optimization of their extraction conditions through the response-surface methodology, were incorporated in quark cheese as natural preservatives and analyzed over 8 days of shelf-life. Both extracts showed antioxidant activity with no toxicity towards primary cell lines at the maximum tested concentration, as well as antibacterial activity, especially against Gram-positive strains. After their incorporation in quark cheese, no significant changes were observed in the nutritional profile and physical traits of the quark cheeses, while the microbial load was highly reduced in the cheese, especially using the extracts obtained from dynamic maceration. Thus, leaf extracts of A. unedo can be promising candidates for use in the food industry as natural preservatives. The authors are grateful to the Foundation for Science and Technology (FCT, Portugal) for financial support through national funds FCT/MCTES to the CIMO (UIDB/00690/2020). M.C. Pedrosa and F. Fernandes thank FCT for their PhD grants (2021.04531.BD, SFRH/BD/145467/2019), S. Heleno and M. Carocho thank FCT for their individual employment program-contract (CEECIND/03040/2017, CEECIND/00831/2018), and L. Barros, M. I. Dias, and R. Calhelha also thank FCT through the institutional scientific employment programcontract for her contract. info:eu-repo/semantics/publishedVersion

“Económicos” are traditional Portuguese pastry products; although their production is low-cost, their nutritional value is equally low. Since it is a widely consumed product in the Trás-os-Montes region, it is important to add value to it without making significant changes to the traditional recipe. Thus, this work has the main objective to increase the nutritional power of “económicos” through the incorporation of chestnut (Castanea sativa) fruit flour. The influence of the incorporation of 9% of chestnut flour as a new ingredient was analysed in terms of physical parameters (texture, colour, pH, water activity and moisture), nutritional content (according to the official AOAC methodology) and chemical parameters (sugars, fatty acids and organic acids) and the ability to control the microbial load over shelf life (32 days). Overall, the addition of the chestnut flour did not drastically change the appearance of the chemical and physical profiles of the cakes, but resulted in a lighter crumb (L*), slight changes in the texture profile, reduction of fat, and most importantly, introduced healthier flour to this inexpensive cake. Moreover, it did not stimu- late the growth of microorganisms (total aerobic mesophiles, coliforms, Bacillus cereus, molds, and yeasts) during the 32 days of storage. The authors are grateful to the Foundation for Science and Technology (FCT, Portugal) for financial support through the national funds FCT/MCTES to CIMO (UIDB/00690/2020). This work was funded by the FEDER-Interreg España-Portugal pro- gramme through the project TRANSCoLAB 0612_TRANS_CO_LAB_2_P and by the European Regional Development Fund (ERDF) through the Regional Operational Program North 2020, within the scope of Project GreenHealth - Digital strategies in biological assets to improve well-being and promote green health, Norte-01-0145-FEDER-000042, to which J. Ueda is thankful for his grant. S. Heleno and M. Carocho thank the FCT for their individual employment program–con- tracts (CEECIND/00831/2018 and CEECIND/03040/2017), while L. Barros is thankful for her institutional scientific contract. F. Fernandes and M. Pedrosa thank the FCT for their PhD grants (SFRH/BD/145467/2019 and SFRH/BD/2021.04531, respectively). info:eu-repo/semantics/publishedVersion

Secondary metabolites are molecules with unlimited applications that have been gaining importance in various industries and studied from many angles. They are mainly used for their bioactive capabilities, but due to the improvement of sensibility in analytical chemistry, they are also used for authentication and as a quality control parameter for foods, further allowing to help avoid food adulteration and food fraud, as well as helping understand the nutritional value of foods. This manuscript covers the examples of secondary metabolites that have been used as qualitative and authentication molecules in foods, from production, through processing and along their shelf-life. Furthermore, perspectives of analytical chemistry and their contribution to metabolite detection and general perspectives of metabolomics are also discussed. The authors are grateful to the Foundation for Science and Technology (FCT, Portugal) for financial support through national funds FCT/MCTES to the CIMO (UIDB/00690/2020). M.C. Pedrosa thanks the “PlantCovid” project for her scholarship. S. Heleno andM. Carocho thank FCT for their individual employment program–contract (CEECIND/00831/2018, CEECIND/03040/2017), and L. Barros also thanks to the national funding by FCT through the institutional scientific employment program–contract for her contract. info:eu-repo/semantics/publishedVersion

Food waste is one of the fundamental issues when it comes to environmental impacts, and this type of waste results in the food’s loss itself, but also that of water, energy, fertilizers, and other resources used for its production. Many vegetable parts are removed from the final product before reaching retail (peels, roots, and seeds), and these raw materials are rich sources of highly valuable molecules such as phytochemicals, minerals, vitamins, and other compounds with health benefits (prevention of several diseases, improvement of the immune system, regulating gastrointestinal transit, and others). Therefore, substantial efforts have been made to find technological solutions to avoid food waste, namely through its reuse in the food chain, thus promoting the circular economy and sustainability. This review focuses on the biggest wastes generated by the food industry, the most common destinations, and case studies applying these by-products or biowaste in the food industry. The authors are grateful to the Foundation for Science and Technology (FCT, Portugal) for financial support through national funds FCT/MCTES to the CIMO (UIDB/00690/2020). M.C. Pedrosa thank FCT for her PhD grant (2021.04531.BD), S. Heleno and M. Carocho thank FCT for their individual employment program contract (CEECIND/03040/2017, CEEC-IND/00831/2018) and L. Barros also thanks FCT through the institutional scientific employment program contract for her contract. info:eu-repo/semantics/publishedVersion

Muffins are snacks made from flour and chocolate and preserved with synthetic additives. Following consumer trends, the search for natural food additives has gained traction. Plants such as rosemary, lemon balm, and oregano were analyzed following an optimization of ultrasound assisted extraction, screened for their antioxidant and antimicrobial activity and incorporated in chocolate muffins, comparing them to synthetic preservatives over the course of 8 days. The nutritional profile, organic and fatty acids, soluble sugars, texture profile, external color and digital imaging of the muffin pores were analyzed. Slight changes were sought for the muffins incorporated with the natural extracts. By means of linear discriminant analysis, rosemary extract was considered the most promising extract to preserve the muffins due to its similarity to potassium sorbate, showing no changes in the muffins it was incorporated in, although it showed a lower amount of phenolic compounds when compared to lemon balm. This research was funded by the Portuguese Foundation for Science and Technology (FCT) and the FEDER-Interreg España-Portugal programme for financial support through the project TRANSCoLAB 0612_TRANS_CO_LAB_2_. The authors are grateful to the Foundation for Science and Technology (FCT, Portugal) for financial support through national funds FCT/MCTES to the CIMO (UIDB/00690/2020). L.B. and R.C.C. also thank the national funding by FCT—Foundation for Science and Technology, through the institutional scientific employment program-contract for their contracts and, M.C., S.H. and J.P. to the national funding by FCT—Foundation for Science and Technology, through the individual scientific employment program-contracts (CEECIND/00831/2018, CEECIND/03040/2017 and CEECIND/01011/2018). The authors are also grateful to FEDER-Interreg España-Portugal programme for financial support through the project TRANSCoLAB 0612_TRANS_CO_LAB_2_. M.C.P. and J.M.U. contributed in the same manner for this manuscript. info:eu-repo/semantics/publishedVersion

The XXI century has brought along many changes in how consumers look at food and perceive their diets. There is an increasing awareness towards what goes into manufacturing these foods, with an important concern being drawn towards food additives. While it is known that additives are needed to preserve or change attributes of food, it is also widely understood that consumers prefer natural additives to synthetic ones, and thus, the industry is looking for alternatives from plant sources. Here, the extraction of 5 different plants (oregano (Origanum vulgare L.), rosemary (Rosmarinus officinalis L.), salvia (Salvia officinalis L.), lemon balm (Melissa officinalis L.) and basil (Ocimum basilicum L.)), was optimized from three extraction types, namely decoction, infusion and cold hydroethanolic (80:20) ultrasound extraction, carried out through Response Surface Methodology (RSM) using Design Expert, pending the analysis of phenolic compounds through HPLC-DAD-ESI/MS. The variables used for RSM were temperature, time of extraction and watts (ultrasound). The extraction with the highest phenolic content for each plant was then selected and screened for its antibacterial and antifungal activity, relying on the microdilution method against foodborne pathogens, before using these extracts as natural food additives in yogurts and muffins. The bacterial species used were Staphylococcus aureus, Bacillus cereus, Listeria monocytogenes, Escherichia coli, Salmonella typhimurium and Enterobacter cloacae, while the fungi species were Aspergillus fumigatus, Aspergillus niger, Aspergillus versicolor, Penicillium funiculosum, Trichoderma viride and Penicillium verrucosum var. cyclopium. Two synthetic and widely used preservatives were also screened against these contaminants, namely sodium benzoate (E211), and potassium metabisulfite (E224), while also confirming the sensitivity of the microbes with known antibiotics. Overall, the plant extracts showed a high inhibition of fungi, with all extracts showing lower minimum inhibition concentrations than both the synthetic preservatives, except for P. verrucosum, where potassium metabisulfite showed the same inhibition capacity. Regarding the antibacterial activity, the most sensitive bacteria to the extracts was S. aureus, where all showed the same activity as potassium metabisulfite. Lemon balm was the best extract of all, showing the same inhibition as sodium benzoate against B. cereus and E. cloacae. Overall, this work proves that plant extracts, obtained though “green” and cheap technologies can be alternatives to synthetic food additives, due to showing the same, or, in some cases, better antimicrobial activity. Furthermore, a mixture of these extracts can result in synergistic effects and improve the antimicrobial activities. The next step in the determination of the efficacy of these extracts is their incorporation in yogurts and muffins, which is ongoing. Acknowledgments Foundation for Science and Technology (FCT, Portugal) for financial support through national funds FCT/MCTES to CIMO (UIDB/00690/2020). S. Heleno and M. Carocho thank FCT for their individual research program-contract (CEECIND/00831/2018; CEECIND/03040/2017), while L. Barros thanks FCT for her institutional scientific employment program-contract.