An innovative oligonucleotide microarray to detect spoilage microorganisms in wine

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.

CyanoStrainChip: A Novel DNA Microarray Tool for High-Throughput Detection of Environmental Cyanobacteria at the Strain Level

Detecting cyanobacteria in environments is an important concern due to their crucial roles in ecosystems, and they can form blooms with the potential to harm humans and nonhuman entities. However, the most widely used methods for high-throughput detection of environmental cyanobacteria, such as 16S rRNA sequencing, typically provide above-species-level resolution, thereby disregarding intraspecific variation. To address this, we developed a novel DNA microarray tool, termed the CyanoStrainChip, that enables strain-level comprehensive profiling of environmental cyanobacteria. The CyanoStrainChip was designed to target 1277 strains; nearly all major groups of cyanobacteria are included by implementing 43,666 genome-wide, strain-specific probes. It demonstrated strong specificity by in vitro mock community experiments. The high correlation (Pearson's R > 0.97) between probe fluorescence intensities and the corresponding DNA amounts (ranging from 1-100 ng) indicated excellent quantitative capability. Consistent cyanobacterial profiles of field samples were observed by both the CyanoStrainChip and next-generation sequencing methods. Furthermore, CyanoStrainChip analysis of surface water samples in Lake Chaohu uncovered a high intraspecific variation of abundance change within the genus Microcystis between different severity levels of cyanobacterial blooms, highlighting two toxic Microcystis strains that are of critical concern for Lake Chaohu harmful blooms suppression. Overall, these results suggest a potential for CyanoStrainChip as a valuable tool for cyanobacterial ecological research and harmful bloom monitoring to supplement existing techniques.

Development and application of a visual microarray for synchronously detecting H5N1, H7N9 and H9N2 avian influenza virus RNA

The aim of this study was to develop a microarray assay for the simultaneous detection of the H5, H7, H9, N1, N9 and N2 genes of the avian influenza virus (AIV) using a Nanogold-streptavidin and silver-stain-enhanced nucleic acid dot-blot hybridisation system. The conserved sequences of H5 genes from H5N1, H7 genes from H7N9, H9 genes from H9N2, N9 genes from H7N9 and N2 genes from H9N2 AIV were cloned, together with that of N1 obtained commercially, and were used as templates for generating the probes using biotin-labeled primers, which targeted the conserved regions of H5, H7, H9, N1, N9 and N2 genes, respectively. The oligonucleotide probes were diluted using the spotting buffer and ddH₂O, and each probe was then spotted to each specific position on the microarray. The PCR products including biotin-labeled lambda, NP, H5, H7, H9, N1, N9 and N2 were mixed, 200 μL of which was then added to the microarray chamber after denaturing. Following a hybridization incubation at 45℃ for 120 min, the microarray was then incubated with nanogold-streptavidin about 4 μg/mL for 30 min. After the supplementary of 200 μL of silver buffer A and silver buffer B in the chamber, the hybridization results were assessed by direct visualization in the dark at room temperature. The microarray assay was optimized and its specificity, sensitivity and stability were evaluated. The optimal conditions comprised a probe concentration of 50 μmol/L, a hybridization temperature of 45℃ and a hybridization time of 2 h. The optimal concentration of nanogold-streptavidin was 4 μg/mL and the optimal staining time was 7 min. The results of specificity evaluation showed that no cross-binding of the probes with each other and no cross-hybridization with Newcastle disease virus, infectious bronchitis virus and infectious laryngotracheitis virus was observed. The optimized microarray assay was significantly more sensitivity than the reverse-transcription PCR assay. The microarray was available after storing at less 90 d at 4 ℃. The optimized microarray assay was validated on clinical specimens and the results showed that it had over 95.6% correlation with reverse-transcription PCR method. Therefore, the microarray assay could be used for the high throughput detection of AIV infections due to H5N1, H7N9 and H9N2.

Non-Saccharomyces Commercial Starter Cultures: Scientific Trends, Recent Patents and Innovation in the Wine Sector

For 15 years, non-Saccharomyces starter cultures represent a new interesting segment in the dynamic field of multinationals and national companies that develop and sell microbial-based biotechnological solutions for the wine sector. Although the diversity and the properties of non- Saccharomyces species/strains have been recently fully reviewed, less attention has been deserved to the commercial starter cultures in term of scientific findings, patents, and their innovative applications. Considering the potential reservoir of biotechnological innovation, these issues represent an underestimated possible driver of coordination and harmonization of research and development activities in the field of wine microbiology. After a wide survey, we encompassed 26 different commercial yeasts starter cultures formulated in combination with at least one non-Saccharomyces strain. The most recent scientific advances have been explored delving into the oenological significance of these commercial starter cultures. Finally, we propose an examination of patent literature for the main yeasts species commercialised in non-Saccharomyces based products. We highlight the presence of asymmetries among scientific findings and the number of patents concerning non-Saccharomyces-based commercial products for oenological purposes. Further investigations on these microbial resources might open new perspectives and stimulate attractive innovations in the field of wine-making biotechnologies.

Synergistic effects of Lactobacillus plantarum and Staphylococcus carnosus on animal food components

Introduction. Various cultures of microorganisms have recently been used to accelerate technological processes. In this regard, it appears highly relevant to study the action of beneficial microorganisms on the components of food systems. Study objects and methods. The study objects included a model mixture of beef muscle and pork fat tissue with 2% salt, as well as a model protein. Lactobacillus plantarum and Staphylococcus carnosus were used in an amount of 1×107 CFU/g of raw material. The compositions of free amino and fatty acids, carbohydrates, and other components were analyzed by liquid and gas chromatography with mass-selective detection. Results and discussion. We studied the effect of L. plantarum and S. carnosus on protein, lipid, and carbohydrate components of food systems based on animal raw materials. We found that the combined effect of the cultures was by 25% as effective as their individual use at 4×109 CFU/kg of raw material. The three-week hydrolysis of proteins to free amino acids was almost a third more effective than when the cultures were used separately. The synergistic effect of L. plantarum and S. carnosus on fat components was not detected reliably. Free monosaccharides formed more intensively when the cultures were used together. In particular, the amount of free lactose almost doubled, compared to the cultures’ individual action. Conclusion. We described culture-caused quantitative changes in the main components of animal-based food systems: amino acids, fatty acids, carbohydrates, and basic organic compounds. Also, we identified substances that can affect the taste and aroma of final products when the cultures are used together or separately. These results make it possible to obtain products with a wide variety of sensory properties.

Potential Use of Silica Nanoparticles for the Microbial Stabilisation of Wine: An In Vitro Study Using Oenococcus oeni as a Model

The emerging trend towards the reduction of SO2 in winemaking has created a need to look for alternative methods to ensure the protection of wine against the growth of undesired species of microorganisms and to safely remove wine microorganisms. This study describes the possible application of silica nanospheres as a wine stabilisation agent, with Oenococcus oeni (DSM7008) as a model strain. The experiment was conducted firstly on model solutions of phosphate-buffered saline and 1% glucose. Their neutralising effect was tested under stirring with the addition of SiO2 (0.1, 0.25, and 0.5 mg/mL). Overall, the highest concentration of nanospheres under continuous stirring resulted in the greatest decrease in cell counts. Transmission electron microscope (TEM) and scanning electron microscopy (SEM) analyses showed extensive damage to the bacterial cells after stirring with silica nanomaterials. Then, the neutralising effect of 0.5 mg/mL SiO2 was tested in young red wine under stirring, where cell counts were reduced by over 50%. The obtained results suggest that silica nanospheres can serve as an alternative way to reduce or substitute the use of sulphur dioxide in the microbial stabilisation of wine. In addition, further aspects of following investigations should focus on the protection against enzymatic and chemical oxidation of wine.

Microbiological Safety and the Management of Microbial Resources in Artisanal Foods and Beverages: The Need for a Transdisciplinary Assessment to Conciliate Actual Trends and Risks Avoidance

Current social and environmental trends explain the rising popularity of artisanal fermented foods and beverages. In contrast with their marketing success, several studies underline a lack of regulations necessary to claim differences occurred from the farm to the fork and to certify high quality and safety standards. Microbial-based fermentative processes represent the crucial phase in the production of fermented foods and beverages. Nevertheless, what are the effects of the application of the "artisanal" category to the management of food fermentations? This opinion paper is built up on this issue by analyzing microbial aspects, instances of innovation, safety issues, and possible solutions. Evidence indicates: (i) a global curiosity to exploit food fermentations as drivers of innovation in artisanal contexts and (ii) an increasing interest of the artisanal producers into management of fermentation that relies on native microbial consortia. Unfortunately, this kind of revamp of "artisanal food microbiology," rather than re-establishing artisanal content, can restore the scarce hygienic conditions that characterized underdeveloped food systems. We highlight that in the scientific literature, it is possible to underline existing approaches that, surpassing the dichotomy between relying on spontaneous fermentation and the use of commercial starter cultures, depict a "third way" to conjugate interest in enhancing the artisanal attributes with the need for correct management of microbial-related risks in the final products.

Climate Changes and Food Quality: The Potential of Microbial Activities as Mitigating Strategies in the Wine Sector

Climate change threatens food systems, with huge repercussions on food security and on the safety and quality of final products. We reviewed the potential of food microbiology as a source of biotechnological solutions to design climate-smart food systems, using wine as a model productive sector. Climate change entails considerable problems for the sustainability of oenology in several geographical regions, also placing at risk the wine typicity. The main weaknesses identified are: (i) The increased undesired microbial proliferation; (ii) the improved sugars and, consequently, ethanol content; (iii) the reduced acidity and increased pH; (iv) the imbalanced perceived sensory properties (e.g., colour, flavour); and (v) the intensified safety issues (e.g., mycotoxins, biogenic amines). In this paper, we offer an overview of the potential microbial-based strategies suitable to cope with the five challenges listed above. In terms of microbial diversity, our principal focus was on microorganisms isolated from grapes/musts/wines and on microbes belonging to the main categories with a recognized positive role in oenological processes, namely Saccharomyces spp. (e.g., Saccharomyces cerevisiae), non-Saccharomyces yeasts (e.g., Metschnikowia pulcherrima, Torulaspora delbrueckii, Lachancea thermotolerans, and Starmerella bacillaris), and malolactic bacteria (e.g., Oenococcus oeni, Lactobacillus plantarum).