Transcriptomic analysis reveals the metabolic mechanism of patulin by Saccharomyces cerevisiae during fermentation

Innovative omics strategies in fermented fruits and vegetables: Unveiling nutritional profiles, microbial diversity, and future prospects

Fermented fruits and vegetables (FFVs) are not only rich in essential nutrients but also contain distinctive flavors, prebiotics, and metabolites. Although omics techniques have gained widespread recognition as an analytical strategy for FFVs, its application still encounters several challenges due to the intricacies of biological systems. This review systematically summarizes the advances, obstacles and prospects of genomics, transcriptomics, proteomics, metabolomics, and multi-omics strategies in FFVs. It is evident that beyond traditional applications, such as the exploration of microbial diversity, protein expression, and metabolic pathways, omics techniques exhibit innovative potential in deciphering stress response mechanisms and uncovering spoilage microorganisms. The adoption of multi-omics strategies is paramount to acquire a multidimensional network fusion, thereby mitigating the limitations of single omics strategies. Although substantial progress has been made, this review underscores the necessity for a comprehensive repository of omics data and the establishment of universal databases to ensure precision in predictions. Furthermore, multidisciplinary integration with other physical or biochemical approaches is imperative, as it enriches our comprehension of this intricate process.

Current insights into yeast application for reduction of patulin contamination in foods: A comprehensive review

Patulin, a fungal secondary metabolite with multiple toxicities, is widely existed in a variety of fruits and their products. This not only causes significant economic losses to the agricultural and food industries but also poses a serious threat to human health. Conventional techniques mainly involved physical and chemical methods present several challenges include incomplete patulin degradation, high technical cost, and fruit quality decline. In comparison, removal of mycotoxin through biodegradation is regarded as a greener and safer strategy which has become popular research. Among them, yeast has a unique advantage in detoxification effect and application, which has attracted our attention. Therefore, this review provides a comprehensive account of the yeast species that can degrade patulin, degradation mechanism, current application status, and future challenges. Yeasts can efficiently convert patulin into nontoxic or low-toxic substances through biodegradation. Alternatively, it can use physical adsorption, which has the advantages of safety, high efficiency, and environmental friendliness. Nevertheless, due to the inherent complexity of the production environment, the sole utilization of yeast as a control agent remains inherently unstable and challenging to implement on a large scale in a practical manner. Integration control, enhancement of yeast resilience, improvement of yeast cell wall adsorption capacity, and research on additional patulin-degrading enzymes will facilitate the practical application of this approach. Furthermore, we analyzed the feasibility of the yeast commercial application in patulin reduction and provided suggestions on how to enhance its commercial value, which is of great significance for the control of mycotoxins in food products.

Detoxification of Mycotoxin Patulin by the Yeast Kluyveromyces marxianus YG-4 in Apple Juice

Patulin (PAT) is a mycotoxin produced by Penicillium species, which often contaminates fruit and fruit-derived products, posing a threat to human health and food safety. This work aims to investigate the detoxification of PAT by Kluyveromyces marxianus YG-4 (K. marxianus YG-4) and its application in apple juice. The results revealed that the detoxification effect of K. marxianus YG-4 on PAT includes adsorption and degradation. The adsorption binding sites were polysaccharides, proteins, and some lipids on the cell wall of K. marxianus YG-4, and the adsorption groups were hydroxyl groups, amino acid side chains, carboxyl groups, and ester groups, which were combined through strong forces (ion interactions, electrostatic interactions, and hydrogen bonding) and not easily eluted. The degradation active substance was an intracellular enzyme, and the degradation product was desoxypatulinic acid (DPA) without cytotoxicity. K. marxianus YG-4 can also effectively adsorb and degrade PAT in apple juice. The contents of organic acids and polyphenols significantly increased after detoxification, significantly improving the quality of apple juice. The detoxification ability of K. marxianus YG-4 toward PAT would be a novel approach for the elimination of PAT contamination.

Identification of a Novel Aflatoxin B1-Degrading Strain, Bacillus halotolerans DDC-4, and Its Response Mechanisms to Aflatoxin B1

Aflatoxin B1 (AFB1) contamination is a food safety issue threatening human health globally. Biodegradation is an effective method for overcoming this problem, and many microorganisms have been identified as AFB1-degrading strains. However, the response mechanisms of these microbes to AFB1 remain unclear. More degrading enzymes, especially of new types, need to be discovered. In this study, a novel AFB1-degrading strain, DDC-4, was isolated using coumarin as the sole carbon source. This strain was identified as Bacillus halotolerans through physiological, biochemical, and molecular methods. The strain's degradation activity was predominantly attributable to thermostable extracellular proteins (degradation rate remained approximately 80% at 90 °C) and was augmented by Cu2+ (95.45% AFB1 was degraded at 48 h). Alpha/beta hydrolase (arylesterase) was selected as candidate AFB1-degrading enzymes for the first time as a gene encoding this enzyme was highly expressed in the presence of AFB1. Moreover, AFB1 inhibited many genes involved in the nucleotide synthesis of strain DDC-4, which is possibly the partial molecular mechanism of AFB1's toxicity to microorganisms. To survive under this stress, sporulation-related genes were induced in the strain. Altogether, our study identified a novel AFB1-degrading strain and explained its response mechanisms to AFB1, thereby providing new insights for AFB1 biodegradation.

New insights into searching patulin degrading enzymes in Saccharomyces cerevisiae through proteomic and molecular docking analysis

Global warming has increased the contamination of mycotoxins. Patulin (PAT) is a harmful contaminant that poses a serious threat to food safety and human health. Saccharomyces cerevisiae biodegrades PAT by its enzymes during fermentation, which is a safe and efficient method of detoxification. However, the key degradation enzymes remain unclear. In this study, the proteomic differences of Saccharomyces cerevisiae under PAT stress were investigated. The results showed that the proteins involved in redox reactions and defense mechanisms were significantly up-regulated to resist PAT stress. Subsequently, molecular docking was used to virtual screen for degrading enzymes. Among 18 proteins, YKL069W showed the highest binding affinity to PAT and was then expressed in Escherichia coli, where the purified YKL069W completely degraded 10 μg/mL PAT at 48 h. YKL069W was demonstrated to be able to degrade PAT into E-ascladiol. Molecular dynamics simulations confirmed that YKL069W was stable in catalyzing PAT degradation with a binding free energy of - 7.5 kcal/mol. Furthermore, it was hypothesized that CYS125 and CYS101 were the key amino acid residues for degradation. This study offers new insights for the rapid screening and development of PAT degrading enzymes and provides a theoretical basis for the detoxification of mycotoxins.

The need for an integrated multi-OMICs approach in microbiome science in the food system

Microbiome science as an interdisciplinary research field has evolved rapidly over the past two decades, becoming a popular topic not only in the scientific community and among the general public, but also in the food industry due to the growing demand for microbiome-based technologies that provide added-value solutions. Microbiome research has expanded in the context of food systems, strongly driven by methodological advances in different -omics fields that leverage our understanding of microbial diversity and function. However, managing and integrating different complex -omics layers are still challenging. Within the Coordinated Support Action MicrobiomeSupport (https://www.microbiomesupport.eu/), a project supported by the European Commission, the workshop "Metagenomics, Metaproteomics and Metabolomics: the need for data integration in microbiome research" gathered 70 participants from different microbiome research fields relevant to food systems, to discuss challenges in microbiome research and to promote a switch from microbiome-based descriptive studies to functional studies, elucidating the biology and interactive roles of microbiomes in food systems. A combination of technologies is proposed. This will reduce the biases resulting from each individual technology and result in a more comprehensive view of the biological system as a whole. Although combinations of different datasets are still rare, advanced bioinformatics tools and artificial intelligence approaches can contribute to understanding, prediction, and management of the microbiome, thereby providing the basis for the improvement of food quality and safety.