Abstract
Flavor compounds present in wine are significant factors in determining consumer preference and style characteristics. The industrial single-strain fermentation model has led to a global crisis of flavor homogenization. The present study was conducted with the objective of providing the wine industry with guidance on the production of wines that exhibit consistent quality and regional style characteristics. To this end, the spatiotemporal succession patterns of fungal communities and Saccharomyces cerevisiae genotypes during Italian Riesling wines were investigated using high-throughput sequencing, culturomics and Interdelta analysis. GC–MS and OAV analysis identified 16 key aroma compounds. Four core strains of Starmerella bacillaris and S. cerevisiae SC1/SC21/SC23 were identified through a top-down approach, and synthetic colonies were constructed for fermentation verification. The results demonstrated that the synthetic community effectively replicated the key aroma chemical characteristics of Italian Riesling wine, providing an innovative fermentation strategy to enhance flavor complexity and market competitiveness of wine.
Keywords: Italian Riesling, spontaneous fermentation, high-throughput sequencing, key aroma compounds, synthetic microbial community
Highlights
- 
•Elucidated dynamics of fungi and S. cerevisiae genotypes during fermentation. 
- 
•Identified sixteen key volatile organic compounds in Italian Riesling wine. 
- 
•Synthetic microbiota could reproduce key aroma compounds of Italian Riesling wine. 
- 
•Developed a microbial community model for synthetic Italian Riesling wine. 
1. Introduction
Wine fermentation is an inherent multiscale biotransformation process driven by microbial communities. Flavor compounds have been identified as critical determinants of consumer preference and serve as key indicators of wine style and typicity, directly reflecting the stylistic characteristics of the wine. In industrial fermentation systems, winemakers typically rely on S. cerevisiae single-strain fermentation. While this ensures process controllability, it often results in a reduction of flavor complexity (Ma, Peng, et al., 2023; Ma, Yu, et al., 2023), contributing to a global crisis of wine flavor homogenization. In order to address this challenge, researchers are employing systems biology approaches, including metagenomics, high-throughput sequencing and metabolomics, with a view to decode the functional networks of indigenous microbiota in spontaneous fermentation systems (Gao et al., 2024;Ma, Peng, et al., 2023; Ma, Yu, et al., 2023). Nevertheless, this approach is inadequate for the provision of production guidance, with the objective of ensuring stable quality and regional style characteristics in the wine industry. The inherent complexity of food fermentation systems, in conjunction with the intricate interactions between fungi and bacteria, continues to pose significant challenges to the precise modulation of flavor compounds (Tian et al., 2022; Wu et al., 2021). Conversely, the bottom-up construction of synthetic microbial communities through the co-cultivation of known microbes under defined conditions provides winemakers with a more precise tool to guide the production of high-quality wine (De Roy et al., 2014). This approach not only elucidates the functional mechanisms of microbial communities but also offers novel solutions for enhancing the stability and diversity of wine flavors. Furthermore, it provides a theoretical framework and technical pathway for the standardized production of regional specialty wines.
Synthetic microbial communities are artificially constructed by co-culturing two or more selected species under a defined medium (Großkopf & Soyer, 2014). The inherent controllability of synthetic communities of microbes enables their functional assembly on demand, thereby facilitating coordination and enhancing synergy. Synthetic microbial communities offer several advantages over single microbes and natural microbial communities. Firstly, the systems are distinguished by their simplicity in structure, clarity in background, and high controllability (Jing et al., 2024), which facilitates their utilization in research and application. Secondly, they demonstrate high stability, and exhibit greater adaptability to changes in external environmental factors (McCarty & Ledesma-Amaro, 2019); Thirdly, they exhibit functional complementarity, whereby microbial interactions enhance metabolic functions, leading to more coordinated overall community functions (Du et al., 2023). To date, research on synthetic microbial communities has been extensively applied to various traditional fermented foods, including broad bean sauce (Jia et al., 2020), sauerkraut (Tlais, Kanwal, et al., 2022), vinegar (Li et al., 2024), traditional sourdoughs (Sabach et al., 2023), and cheese microbiomes (Cosetta & Wolfe, 2020), Chinese liquor (Du et al., 2023), soy sauce (Det-Udom et al., 2019), rice wine (Peng et al., 2025), and Huangjiu (Peng et al., 2024). However, research on synthetic microbial communities in wine fermentation is still in its infancy. Consequently, the development and control of synthetic microbial communities represent an effective approach to ensure the quality and safety of fermented foods. The construction of synthetic microbial communities enables precise control of the fermentation process, thereby providing the wine industry with an innovative solution to enhance product quality, stability, and style characteristics.
Italian Riesling wine is held in high esteem by consumers due to its distinctive flavor and aroma. However, further investigation is warranted into the mechanisms of formation of its flavor compounds and the dynamic changes in microbial communities. The application of high-throughput sequencing and culture-dependent techniques has been demonstrated to facilitate a more comprehensive understanding of the composition and function of microbial communities during the fermentation process. This, in turn, provides a scientific basis for the optimization of vinification processes. In this study, gas chromatography–mass spectrometry (GC–MS) was employed to conduct qualitative and quantitative analysis of the aroma compounds in Italian Riesling wine, followed by identification key flavor compounds. The application of high-throughput sequencing and culture-dependent technology facilitated the dynamic monitoring of microbial communities during the fermentation process. This approach enabled the analysis of the composition and alterations of microbial communities across various stages of the fermentation process. The construction of synthetic microbial communities was achieved through the screening and combination of core microbial species. This approach enabled the simulation of the functions of natural microbial species. The application effects of these synthetic communities in the fermentation process were subsequently verified. This study proposes novel technical approaches for the vinification of Italian Riesling wine and provides references for the quality control and flavor optimization of other fermented foods. The employment of synthetic microbial communities has been demonstrated to enable precise regulation of the fermentation process. This, in turn, has been shown to propel technological advancement and industrial upgrading within the domain of fermented foods.
2. Materials and methods
2.1. Spontaneous fermentation and sampling
Italian Riesling grapes utilized in this experiment were sourced from Penglai, Shandong, China (37.79°N, 120.77°E). During the harvesting season (September 2022), samples were collected from five specific locations in the vineyard (One central area and four corner areas) using a five-point sampling method. Following the stipulated wine production requirements, the Italian Riesling grapes selected for this experimental study underwent manual a series of meticulous procedures. The process entailed a series of manual operations, including destemming, pressing, and crushing, culminating in a comprehensive clarification treatment. During the process of grape crushing, 40 mg/L SO₂ (industrially standard) was added to prevent interference from spoilage microorganisms during fermentation, and 20 mg/L pectinase was added to improve juice yield. The entire process was conducted under strictly controlled conditions to ensure sterility, with all equipment, operators, fermentation tanks, and the fermentation environment being subjected to rigorous sterilization procedures. Upon achieving turbidity (NTU) levels of 200, the grape juice (total sugar 165 g/L, total acid 7.62 g/L, pH 3.30) was transferred into three pristine, aseptic 20 L glass jars for the initiation of spontaneous fermentation. The fermentation temperature was meticulously regulated at a range of 14–17 °C, and the fermentation process was terminated when residual sugar levels diminished to below 4 g/L. Each fermentation tank underwent three biological replicates. Given that the total sugar content of the must was less than 200 g/L, 35 g/L of table sucrose was added to the fermenter during the peak fermentation phase to minimize the impact on the fungi. The fermentation progress was meticulously monitored by conducting specific gravity measurements on a twice-daily basis. Sampling was conducted at various stages of the fermentation process, specifically when the NTU reached 200 (F1); when a decrease in total sugar was observed (F2); when total sugar consumption reached 30 % (F3); when total sugar consumption reached 80 % (F4); and when total sugar was below 4 g/L (F5). The detailed procedure was as follows: prior to sampling, the area surrounding the sampling port of the fermentation tank was meticulously wiped and sterilized using a 75 % ethanol solution. An alcohol lamp was also ignited in the operational area to establish a relatively sterile environment for sampling. Subsequently, a sterilized pipette was employed to draw the sample, which was then transferred into a pre-sterilized centrifuge tube. It was crucial to highlight that each fermentation tank was assigned exclusive aseptic pipettes and centrifuge tubes, thereby preventing cross-contamination among different samples. All samples were stored at −80 °C until analysis. A proportion of the samples was then subjected to high-throughput sequencing, while the remainder was analyzed for its basic physicochemical properties.
2.2. Determination of physical and chemical parameters
Titratable acidity, pH, and volatile acidity were measured directly according to the Chinese national standard GB 15038-2006. The assay of yeast assimilable nitrogen (YAN) was conducted utilizing the 12,807-AMMONIA and 12,809-PAN kits (Biosystem) in conjunction with a fully automated analyzer (Biosystems, Barcelona, Spain). The samples were subjected to a centrifugal process at a speed of 12,000 rpm for five minutes. Thereafter, the upper layer of the samples was analyzed following the instructions provided in the kit. The quantification of glucose, fructose, organic acids, glycerol, and ethanol was conducted via high-performance liquid chromatography (LC1260, Agilent Technologies Co. Ltd., USA); the specific method is detailed in Huang et al. (2023).
2.3. Determination of volatile compounds
To prepare samples, 1.2 g NaCl was weighed into a 20 mL glass headspace (HS) vial pre-loaded with 5 mL of sample. A 10 μL aliquot of 4-methyl-2-pentanol (1.013 g/L) was then introduced as internal standard before the vial was hermetically sealed with a magnetic screw cap equipped with a silicone septum. The extraction of volatile compounds was strictly performed using Headspace Solid-Phase Microextraction (HS-SPME). Key operational parameters, including fiber coating type, sample incubation temperature and time, extraction time, and desorption time, were slightly modified based on our research group's established and fully validated protocol (Chen et al., 2024). After equilibrating the sample at 40 °C for 30 min, the SPME fiber was inserted and exposed for 30 min under continuous agitation at 500 rpm. Following extraction, the fiber was automatically introduced into the injector for thermal desorption over 8 min, with helium as the carrier gas at a flow rate of 1 mL/min. The injector temperature was maintained at 250 °C, and sample introduction was performed in split mode (5:1). The extracted volatiles were analyzed on a Trace 1610 GC hyphenated to an ISQ 7610 MS (both Thermo Fisher Scientific, USA). The gas chromatography temperature program was set as follows: initial temperature 50 °C held for 1 min, then ramped at 3 °C/min to 220 °C and held for 5 min. The mass spectrometer interface temperature was set to 250 °C, while the ion source and quadrupole temperatures were maintained at 250 °C and 150 °C, respectively. Electron ionization (EI) mode was used with an ionization energy of 70 eV. Compound identification was achieved by matching mass spectra to the NIST20.L library and cross-referencing retention times and diagnostic m/z fragments. Calibration standards were prepared in a synthetic wine matrix (15 % v/v ethanol, 5 g/L tartaric acid) whose pH was accurately adjusted to 3.50 with 1 M NaOH. Volatiles were quantified by the internal standard method using external calibration curves. Compounds without available standards were quantified using surrogates of similar chemical structure and carbon number. For detailed quantitative information regarding the linear fitting, the R2 values, linear ranges, odor attributes, and odor categories of the volatile compounds analyzed in this study are provided in Supplementary Table 1. Volatile compounds lacking corresponding reference standards (2,4-Di-tert-butylphenol, ethyl benzoate and propanoic acid) were quantified using calibration curves of compounds with the same functional group and similar carbon chain length.
2.4. Total DNA extraction and high-throughput sequencing
The total DNA of the microbiome was extracted using the HiPure Stool DNA Kit (Magen, Guangzhou, China), in accordance with the manufacturer's instructions, with final elution in 80 μL of preheated (70 °C) Buffer AE. The concentration of DNA was determined by measuring the optical density of the samples at 260 nm using a NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). The integrity and quality of the samples were evaluated by subjecting them to 1 % agarose gel electrophoresis. The genomic DNA was dispatched to Genedenovo Biotech Ltd. The amplification and sequencing were conducted at the Guangzhou Research Hub (https://www.genedenovo.com/). The filtration and processing of data were conducted in accordance with the methodologies outlined in preceding studies (Zhang, Zhuang, et al., 2025; Zhang, Zhao, et al., 2025). Samples for high-throughput analysis were prepared in triplicate.
In order to amplify the fungal ITS2 (Internal Transcribed Spacer) region, the primers ITS3_KYO2F (5′-GATGAAGAACGYAGYRAA-3′) and ITS4R (5′-TCCTCCGCTTATTGATATATGC-3′) were utilized. The PCR reactions were performed in triplicate using a 50 μL mixture comprising 5 μL of 10 × KOD Buffer, 5 μL of 2.5 mM dNTPs, 1.5 μL of each primer (5 μM), 1 μL of KOD Polymerase, and 100 ng of template DNA. The amplification was initiated with an initial denaturation step at 95 °C for 2 min, followed by 27 cycles of denaturation at 98 °C for 10 s, primer binding at 62 °C for 30 s, and extension at 68 °C for 30 s.
2.5. Screening, culture, and identification of fungi
The samples were diluted using a sterile saline solution via a gradient dilution technique (F1: 102–104; F2: 104–106; F3: 105–107; F4: 105–107; F5: 105–107). The diluted solution was thoroughly mixed and 1000 μL of this was applied to WLN nutrient agar (containing 100 mg/L chloramphenicol to inhibit bacterial growth). The agar was then subjected to an incubation process at a temperature of 28 °C for a period of 2–3 days (three parallels). The most suitable dilution was selected, and the total colony count per milliliter was determined. The WLN agar plates were observed post-incubation at 28 °C for a period of 5–6 days. Thereafter, the colony color and morphology were recorded for subsequent classification and identification. The colonies, which exhibited a range of morphologies, were meticulously enumerated and documented individually. The selection of 3–5 WLN culture types for pure culture was based on each morphological stage of Italian Riesling spontaneous fermentation. Purely isolated strains were cultivated in YPD medium at 28 °C for 2 days. Glycerol (final concentration 25 %) was added, and the strains were stored at −80 °C.
The genomic DNA was extracted using the Fungi Genomic DNA Extraction Kit (Beijing Solarbio Science & Technology Co., Ltd.) in accordance with to the manufacturer's instructions. Universal primers NL1 and NL4 were utilized in the amplification and sequencing of the 26S rDNA D1/D2 region. The identification of 26S rDNA yeast strains was facilitated by the utilization of NL1 (5′-GCATATCAATAAGCGGAGGAAAAG-3′) and NL4 (5′-GGTCCGTGTTTCAAGACGG-3′). The PCR reaction was performed in a 50 μL reaction volume, comprising 25 μL 2 × Rapid Taq Master Mix, 2 μL of each 10 μM forward and reverse primer, 1 μL of DNA template (200 ng), and 20 μL of sterile deionized water. PCR program was 95 °C for 3 min (pre-denaturation), 95 °C for 15 s, 55 °C for 45 s, 72 °C for 30 s, and 72 °C for 5 min (final extension). A 4 μL of the PCR product was subjected to electrophoresis on a 1 % agarose gel for approximately 25 min. Positive products were subsequently sent to Beijing Genomics Co., Ltd. for purification and sequencing. The sequences were analyzed using the BLAST tool available at NCBI (https://blast.ncbi.nlm.nih.gov/Blast.cgi). The range of gene sequence similarity was from 99 % to 100 %, which is consistent with the standard of ≤ 1 % difference within the same species.
Strains identified as S. cerevisiae were subsequently subjected to Interdelta fingerprinting. The primer sequence employed was delta12 (5′-TCAACAATGGAATCCCAAC-3′) and delta21 (5′-CATCTTAACACCGTATGA-3′). The PCR reaction system comprised, 12.5 μL 2 × Rapid Taq Master Mix, 1 μL upstream primer (10 μM), 1 μL downstream primer (10 μM), 0.7 μL (80 ng/μL) DNA template, and sterile deionized water was made up to 25 μL. The thermal cycling parameters for the PCR comprised pre-denaturation at 95 °C for 4 min, denaturation at 95 °C for 30 s, reversion at 46 °C for 30 s, extension at 72 °C for 90 s, and a total of 35 cycles, finally, 72 °C was used to make up for the flatness for 10 min. The amplified products were then subjected to 2 % m/v agarose gel electrophoresis for 1 h at a constant voltage of 120 V. The subjects were observed and photographed using a UV imager.
2.6. Fermentation of synthetic microbial communities
In a 250 mL flask, 150 mL of filtered (sterile 0.22 μm filter membrane) Italian Riesling grape juice (harvested in September 2024 from Penglai, Shandong) was subjected to fermentation at 18 °C (Since the total sugar content of the grape juice reached 200 g/L, no sucrose was added). The flask was inoculated with an 18-h pre-culture; specific inoculation details are provided in Table 1. Besides the aforementioned experiments, single-strain fermentations were performed using the commercial S. cerevisiae F15 and three indigenous strains (SC1, SC21, and SC23). The progression of fermentation was monitored by tracking the loss of CO₂, with data recorded at 24-h intervals. A total of three biological replicates were conducted for each fermentation vessel. The fermentation process was considered to have reached its conclusion when the rate of weight loss remained below 0.2 g/L for two consecutive days.
Table 1.
Microbial inoculation concentrations in the fermentation of Italian Riesling wines using a synthetic microbial community.
| Microbial inoculation (CFU/mL) | Starmerella bacillari (SB) | Saccharomyces cerevisiae (SC1) | Saccharomyces cerevisiae (SC21) | Saccharomyces cerevisiae (SC23) | 
|---|---|---|---|---|
| All | 1 × 106 | 1 × 106 | 1 × 106 | 1 × 106 | 
| All-ΔSB | 1 × 106 | 1 × 106 | 1 × 106 | |
| All-ΔSC3 | 1 × 106 | 1 × 106 | 1 × 106 | |
| All-ΔSC21 | 1 × 106 | 1 × 106 | 1 × 106 | |
| All-ΔSC23 | 1 × 106 | 1 × 106 | 1 × 106 | 
2.7. Statistical analysis
The results obtained are presented as mean ± standard deviation. Microbial count data were analyzed in CFU/mL units. Fungal identification results were submitted to the NCBI database (https://www.ncbi.nlm.nih.gov/) for sequence alignment and analysis. SPSS 25 (IBM® SPSS® Statistics, NY, USA) and GraphPad Prism 8.0.2 (GraphPad Software, Inc., La Jolla, CA, USA) were used to visualize fungal composition, liquid chromatography data, and volatile components, including one-way ANOVA for significant differences in raw data. Principal component analysis (PCA) was used to analyze volatile differences in Italian Riesling at different spontaneous fermentation stages, with visualization facilitated via SIMCA 14.1 (Umetrics AB, Umeå, Sweden). The O2PLS model was constructed utilizing an online platform (https://www.omicshare.com/) to explore relationships between microbes and flavor compounds. Heatmaps were visualized using TBtools (Toolbox for Biologists; version 2.042, China). A correlation analysis was performed between aroma-active compounds and yeasts, with ggplot2 software utilized in R (version 3.4.0) for graphical representation.
3. Results and discussion
3.1. Dynamics of metabolites during wine fermentation
The physicochemical parameters of Italian Riesling during spontaneous fermentation at various stages are presented in Table 2. Throughout spontaneous fermentation, reducing sugars declined sharply; at the terminal stage (F5) total residual sugar fell below 4 g/L, signifying successful fermentation yet leaving a trace of residual sweetness. As sugars were depleted, ethanol and glycerol accumulated significantly, attaining final concentrations of 11.57 ± 0.01 g/L and 7.96 ± 0.23 g/L, respectively. YAN was abundant when fermentation initiated, and it declined steadily and markedly throughout fermentation. Strikingly, YAN stabilized during the terminal phase (F4-F5), ceasing its decline, an observation attributed to supplementary nitrogen released via late-stage yeast autolysis and protein hydrolysis (Christofi et al., 2022; Romano et al., 2022). Overall, total acidity and pH exhibited inverse trends. Initially, tartaric and malic acids dominated the organic-acid profile, with succinic acid presented at lower levels, which was consistent with previous reports (Ding et al., 2024). Throughout fermentation, citric acid levels remained relatively constant, while tartaric acid levels exhibited a marked increase followed by a significant decrease. Malic acid levels remained stable in the early fermentation phase (stages F1-F2), but decreased markedly from stage F3 onward, reaching relatively low levels by the end of fermentation. Succinic acid levels remained relatively constant in the first three stages, increased significantly at F4, and reached 1.04 ± 0.05 g/L at F5. Lactic acid was produced in the late fermentation stage, while acetic acid was generated during the active fermentation phase. These alterations in physicochemical properties are closely associated with microbial dynamics during fermentation. The marked shifts in the aforementioned physicochemical indices (sugars, ethanol, glycerol, YAN, organic acids, and pH) are intimately linked to the metabolic activity and population succession of yeast communities throughout fermentation.
Table 2.
Changes in physicochemical indicators during spontaneous fermentation of Italian Riesling.
| Sample | F1 | F2 | F3 | F4 | F5 | 
|---|---|---|---|---|---|
| Glucose (g/L) | 80.72 ± 2.09a | 71.72 ± 0.48b | 56.39 ± 0.22c | 4.58 ± 0.08d | 0.93 ± 0.03e | 
| Fructose (g/L) | 85.73 ± 0.67a | 77.67 ± 0.64b | 63.94 ± 0.22c | 34.86 ± 0.15d | 1.08 ± 0.05e | 
| YAN (mg/L) | 249.33 ± 3.06a | 110.67 ± 1.15b | 56.67 ± 1.15c | 14.67 ± 1.15d | 14.67 ± 1.15d | 
| Total acid (g/L) | 7.62 ± 0.05d | 8.01 ± 0.07c | 8.63 ± 0.08a | 8.23 ± 0.03b | 7.53 ± 0.04d | 
| pH | 3.3 ± 0.01a | 3.26 ± 0.01b | 3.08 ± 0.01d | 3.08 ± 0.01d | 3.23 ± 0.02c | 
| Citric acid (g/L) | 0.64 ± 0.00a | 0.64 ± 0.00a | 0.64 ± 0.00a | 0.55 ± 0.00a | 0.51 ± 0.00a | 
| Tartaric acid (g/L) | 2.73 ± 0.12bc | 2.97 ± 0.06a | 2.77 ± 0.06b | 2.78 ± 0.03b | 2.61 ± 0.01c | 
| Malic acid (g/L) | 2.36 ± 0.06a | 2.32 ± 0.15a | 2.12 ± 0.02b | 2.1 ± 0.00b | 1.9 ± 0.01c | 
| Succinic acid (g/L) | 0.9 ± 0.14b | 0.87 ± 0.06b | 0.87 ± 0.06b | 1.12 ± 0.03a | 1.04 ± 0.05a | 
| Lactic acid (g/L) | – | – | – | 0.24 ± 0.00a | 0.27 ± 0.04a | 
| Acetic acid (g/L) | – | – | 0.08 ± 0.00c | 0.14 ± 0.00b | 0.18 ± 0.01a | 
| Glycerol (g/L) | – | 0.47 ± 0.02d | 1.99 ± 0.06c | 5.69 ± 0.21b | 7.96 ± 0.23a | 
| Ethanol (g/L) | – | 0.6 ± 0.01d | 2.41 ± 0.08c | 8.51 ± 0.08b | 11.57 ± 0.01a | 
3.2. Dynamic succession of fungal microbial during spontaneous fermentations
3.2.1. High-throughput sequencing analysis
A high-throughput sequencing analysis was conducted in order to ascertain succession patterns of fungal communities during Italian Riesling spontaneous fermentation. Subsequent to the implementation of Usearch quality control, a total of 1,894,558 high-quality fungal effective tags were obtained and clustered into 879 OTUs. Rarefaction curves were stabilized, with high-quality sequence coverage exceeding 99 %, indicating sufficient sequencing depth for reliable microbial community analysis (see Supplementary material Fig. S1 A) (Ding et al., 2024). The rank abundance curve flattened during descent, indicating a more uniform species distribution in the community (Supplementary material Fig. S1B). As the fermentation process unfolded, substantial alterations manifested within the grape juice microbiome. The fungal community α-diversity exhibited a decline in the Shannon index (Fig. 1A), with the lowest diversity observed at F4, while Chao1 richness exhibited fluctuations (Fig. 1B), a phenomenon that may be attributable to the fermentation conditions. The PCoA, based on Bray-Curtis distances, demonstrated that the first two coordinates accounted for 99.93 % of the total variance. F1 was found to be distinctly separate from the other stages, and F3 and F4 were found to be close but non-overlapping, indicating significant changes in fungal communities throughout the fermentation process (Fig. 1C). This study also employed permutational multivariate analysis of variance (PERMANOVA) using the Adonis function to assess differences in fungal communities during spontaneous fermentation. The results (R2 = 0.9973, P = 0.001) indicated significant differences in the fungal communities across the five key stages of the fermentation process. At the phylum level, the predominance of fungi was observed (Supplementary material Fig. S1C). At the genus level, F1 was dominated by Cladosporium, Colletotrichum, and Saccharomyces, while Hanseniaspora accounted for only 1.10 % (Fig. 1D). Cladosporium and Alternaria, plant pathogens existing as epiphytes on grapevines and other hosts, often infect grapes with soluble solids >15 % or mechanical damage (Jiao et al., 2022). Furthermore, Cladosporium infection in grapes has been demonstrated to result in a loss of fruit aroma and a negative impact on red wine color (Liu et al., 2025). Following the onset of fermentation, Saccharomyces gradually became the dominant taxa within the community, whilst other taxa underwent a decline (Fig. 1D). This observation was consistent with the findings of several studies that have demonstrated an increase in Saccharomyces increases during spontaneous fermentation, while other fungal communities decrease in abundance but remain present by the end of the fermentation (Ding et al., 2024; Gao et al., 2024;Wei, Chen, et al., 2022; Wei, Ding, et al., 2022). Venn diagram analysis revealed 61 genera shared across all five stages, 37 of which were unique to F1, 4 to F2, 3 to F3, 2 to F4, and 27 to F5 (Supplementary material Fig. S1D).
Fig. 1.
Analysis of fungal community diversity during spontaneous fermentation of Italian Riesling. (A) Shannon index of the fungal community. (B) Chao1 index of the fungal community. (C) Principal Coordinate Analysis (PCoA) based on weighted UniFrac between fungal communities. (D) Relative abundance changes based on genus level (Top 10 relative abundances).
3.2.2. Fungi culture group identification analysis
The objective of this study was to characterize a synthetic microbial community. In order to achieve this objective, a comprehensive examination of culture groups was conducted in fermentation broths from various stages of Italian Riesling fermentation. The initial classification was performed based on morphological features on the WLN medium (Supplementary material Fig. S2), followed by the selection of representative strains with distinct WLN phenotypes for molecular identification, resulting in the isolation and purification of 157 microbial strains (Supplementary material Table S2). The structure of the cultivable fungal community demonstrated pronounced dynamic shifts throughout the fermentation process. Cultivation-based identification revealed six fungal species from five genera: S. cerevisiae, S. bacillaris, Hanseniaspora uvarum, Hanseniaspora vineae, Pichia kudriavzevii, and Alternaria alternata (Fig. 2A). In grape juice, S. bacillaris was the predominant fungal species (60 % of total), followed by S. cerevisiae, with H. uvarum representing a mere 6.67 % of the community. During the initial fermentation stage, S. cerevisiae rapidly became the dominant microbial group in alcoholic fermentation (99.72 % of total colony level), while the relative abundance of S. bacillaris decreased sharply. Throughout the F3 and F4 stages, S. cerevisiae maintained its dominance in fermentation, with a continuous increase in relative abundance. By the end of fermentation, S. cerevisiae had become the sole surviving microbial species in the fermentation broth. S. cerevisiae exerts inhibitory effects on other microorganisms through multiple mechanisms, such as the production of short-chain fatty acids and killer toxins (glycoproteins). Its specific antagonistic actions play a regulatory role in ecosystem dynamics (Boynton & Greig, 2016).
Fig. 2.
Analysis of culture-dependent fungal communities during the spontaneous fermentation of Italian Riesling. (A) Changes in the abundance of the fungal community of species during fermentation. (B) Changes in the number of different genotypes of S. cerevisiae during fermentation.
Regardless of detection method, S. cerevisiae persisted as the dominant species throughout fermentation. Interdelta analysis of 150 S. cerevisiae isolates revealed 24 distinct genotypes (Supplementary material Fig. S3C). As illustrated in Fig. 2C, the temporal dynamics of S. cerevisiae genotypes differed markedly across fermentation stages. Notably, intraspecific diversity peaked during F3 and F5, corroborating earlier reports (Sun et al., 2015). The findings reveal that wine alcoholic fermentation is governed not by a single S. cerevisiae strain, but by a dynamic and intricate microbial succession. Strain SC3 displayed continuous fitness and peaked in the final stage and SC4 dominated the mid-early phase yet was ultimately outcompeted. Concomitantly, a distinct genotype cluster (SC18–SC30) surfaced late in fermentation, an outcome plausibly driven by escalating environmental stresses (elevated ethanol, nutrient exhaustion, etc.) that foster genetic diversification, competitive exclusion, and adaptive selection, possibly involving gene exchange (González et al., 2023). These strain dynamics may critically impact fermentation kinetics and ultimately shape wine flavor profiles and final quality.
Discrepancies between high-throughput sequencing and culturomics analysis was attributed to several factors. The two approaches utilized different primer sets for the purpose of PCR amplification of distinct regions. NL primers target the D1–D2 domain of the 26S rRNA gene, affording enhanced discrimination between yeast species. Conversely, ITS primers span the highly variable ITS1 and ITS2 regions of the fungal rRNA operon, rendering them ideal for taxonomic assignment and species-level identification of fungi. Furthermore, it has been demonstrated that certain species may transition to a viable but non-culturable state under environmental stress in high-stress fermentation environments, thereby preventing their growth on artificial media (He et al., 2022). This phenomenon may provide a rationale for the inability to identify some species using culture-dependent approaches (Divol et al., 2012). HTS is particularly effective for characterizing diversity within complex polymicrobial communities. Yet, its sensitivity toward low-abundance taxa embedded within dominant populations is constrained, resulting in diminished detection likelihood, and primer bias can render some species refractory to amplification (He et al., 2022). Moreover, HTS fails to distinguish viable from non-viable cells, and species-level identification is strongly contingent upon the fidelity of the underlying databases. Remain unculturable using currently available media. Furthermore, substantial proportions of microbial taxa remain unculturable by conventional cultivation media (Yan et al., 2013; F. Zhang et al., 2018), leading to systematic under-representation of their diversity in culture-dependent surveys (Lu et al., 2020; Yan et al., 2013). Accordingly, integrating culture-dependent and culture-independent strategies is indispensable for a holistic and accurate characterization of microbial communities, given their complementary insights. Concurrently, traditional cultivation offers the requisite axenic isolates that underpin the assembly of synthetic microbial consortia.
3.3. Composition of spontaneous wine aromas
The study identified 50 aroma compounds across 10 categories (Supplementary material Table S3). PCA demonstrated that fermentation significantly altered aroma compounds, with the first two principal components explaining 87.7 % of the variation (Fig. 3A). During the process of vinification, the transformation of grape juice into wine is accompanied by the release of various volatile compounds, which collectively contribute to the formation of the wine's aroma profile. Higher alcohols, organic acids, and esters are the key aromatic compounds in wine, significantly influencing its aromatic profile and sensory attributes (He et al., 2023). Major volatile compounds exhibited marked dynamic changes throughout alcoholic fermentation (P < 0.05). Higher alcohols, fatty acids, and esters exhibited pronounced accumulation from start to finish (Fig. 3B). Carbonyls followed a biphasic trajectory, and their concentration decreased in the early stage of fermentation, but increased significantly at the end of fermentation. Conversely, terpenes declined below their initial must concentrations at the final stage, implying partial degradation or biotransformation. Remaining compound classes accumulated steadily, reaching maximal concentrations at fermentation completion (Fig. 3B). Collectively, these dynamics underscore the decisive role of Saccharomyces metabolism in shaping the wine's aromatic profile.
Fig. 3.
Analysis of volatile aroma during spontaneous fermentation of Italian Riesling. (A) PCA analysis of volatile aroma of sample varieties at different stages. (B) Changes of different categories of aroma substances during fermentation.
As indicated by the odor activity values (OAV > 1), the following compounds were identified as key contributors to the aroma profile of Italian Riesling wine: phenylethyl alcohol, 1-propanol, isoamyl alcohol, phenol, 2-methoxy-4-ethylphenol, 2,4-di-tert-butylphenol, nonanal, geraniol, ethyl acetate, isoamyl acetate, ethyl butyrate, ethyl hexanoate, ethyl caprylate, isobutyric acid, octanoic acid, and n-decanoic acid. Fatty alcohols such as 1-propanol, isobutyric acid and isopentanol are considered to be representative of those found in wine. 1-propanol has been shown to contribute a mature fruit and alcoholic aroma to wine, while isobutyl alcohol and isoamyl alcohol may impart undesirable alcoholic and nail polish-like pungent notes (Liu et al., 2023). Phenylethyl alcohol has been shown to contribute a desirable honey and rose-like aroma to wine (Liu et al., 2023). Research suggests that higher alcohol levels below 300 mg/L promote the expression of floral and fruity aromas in wine, enhancing its aromatic complexity, whereas levels exceeding 400 mg/L may result in undesirable odors (Lai et al., 2023). Brettanomyces/Dekkera bruxellensis has been observed to produce 4-ethylphenol and 2-methoxy-4-ethylphenol during growth and metabolism, which can negatively affect wine sensory attributes (Childs et al., 2015). The study have also shown that 2-methoxy-4-ethylphenol can provide fragrance (Wang et al., 2023). This may provide a rationale for the elevated levels of volatile phenols observed in this study. Geraniol, nerol, citronellol, and α-terpineol have been identified as the most prevalent compounds in Muscat wines (Chen et al., 2021). The study identified five terpene compounds, among which d-limonene, citronellol, and geraniol contributed to the aroma of Italian Riesling wine, with geraniol being especially significant. While a small fraction of esters accumulate during grape maturation, most esters are synthesized by yeast during alcoholic fermentation. These compounds characteristically contribute fruity and floral notes to wine, thereby playing a pivotal role in shaping its aromatic profile (Dzialo et al., 2017). Fatty acid metabolism is the primary pathway for the formation of volatile acids, including isobutyric acid, octanoic acid, and propionic acid. Fatty acids function as precursors to fatty acid ethyl esters, and their metabolic evolution exerts a substantial influence on the synthesis of ethyl ester compounds in wine. These compounds elucidate the role of aroma substances in Italian Riesling wine and their influence on its sensory attributes. Elucidation of the origins and contributions of these compounds offers a scientific foundation for refining fermentation processes and improving the aromatic quality of wine.
3.4. Screening and characterization of core fungi populations
In order to delineate the core fungi community in Italian Riesling wine fermentation, O2PLS modeling and Pearman correlation analysis were employed. These tools analyzed the relationships between fungal communities, species, S. cerevisiae genotypes, and key volatile flavor compounds during spontaneous fermentation, thereby identifying key fungi communities. In the model associating fungal communities with key volatile compounds, the X matrix (key flavor compounds) explained 0.976 of the variance, while the Y matrix (fungal microbiota) explained 0.991 (R2Xcorr = 0.894, R2Ycorr = 0.991), confirming a robust model fit. The results indicated that Saccharomyces, Mycosphaerella, Penicillium, Aspergillus, and Aureobasidium exhibited correlations with key aroma compounds, excluding geraniol. In contrast, Hanseniaspora, Colletotrichum, Papiliotrema, Alternaria, and Cladosporium demonstrated correlations exclusively with geraniol (Fig. 4A).
Fig. 4.
Correlation analysis between important functional microbiota and key aroma compounds during spontaneous fermentation. (A) Correlation analysis of O2PLS model of microorganisms with key aroma compounds based on amplicon sequencing (Top 10 relative abundances). (B) Correlation analysis of O2PLS model of microorganisms with key aroma compounds based on culture-dependent methods. (C) Heat map of Pearman's correlation between different genotypes of S. cerevisiae and key aroma compounds (Table S5).
In the model linking fungal culturomics microbiota to key volatile compounds, the X matrix (key flavor compounds) accounted for 0.946 of the variance, while the Y matrix (fungal culturomics microbiota) accounted for 0.968 (R2Xcorr = 0.946, R2Ycorr = 0.796), indicating a robust model fit. The results of the study demonstrated that, non-Saccharomyces, S. bacillaris exhibited significant correlations with key aroma compounds. S. bacillaris, a non-Saccharomyces naturally present on grape berry surfaces, has been shown to enhance terpene production (Wang et al., 2024). Furthermore, H. vineae, P. kudriavzevii, and H. uvarum showed significant correlations with geraniol, while S. cerevisiae exhibited strong correlations with key aroma compounds (such as 2-methoxy-4-ethylphenol, octanoic acid, ethyl caprylate, isobutyric acid, 2,4-Di-tert-butylphenol, n-Decanoic acid and so on, Fig. 4B). Concurrently, S. bacillaris dominated the grape must microbiota, whereas S. cerevisiae prevailed throughout alcoholic fermentation. Overall, S. cerevisiae and S. bacillaris exhibited significant correlations with the majority of core volatile compounds, with S. cerevisiae being particularly notable, a finding that aligns with previous research (Ma, Peng, et al., 2023; Ma, Yu, et al., 2023).
In further pursuit of the correlations disparate different S. cerevisiae genotypes and key aroma compounds, this study has constructed a correlation heatmap using the Pearson correlation coefficient for dominant genotypes and key aroma compounds. The results indicated that S. cerevisiae SC1 showed significant positive correlations with ethyl caprylate, isobutyric acid, n-decanoic acid, 2,4-Di-tert-butylphenol, and octanoic acid. S. cerevisiae SC20, SC21 and SC23 exhibited positive correlations with all key aroma compounds, except geraniol, exhibiting significant positive correlations, especially with ethyl acetate, phenol, 1-propanol, isoamyl acetate, isoamyl alcohol, ethyl hexanoate, phenyl ethanol, and nonanal. Furthermore, SC21 showed significant positive correlations with ethyl caprylate and 2,4-Di-tert-butylphenol (Fig. 4C). Although SC20 exhibited significant correlations with aroma compounds comparable to SC21 and SC23, its correlation strengths were lower than those observed for SC21 and SC23. Consequently, strains SC21 and SC23 were prioritized for selection. While SC1 exhibited complementary metabolic functions to SC21 and SC23, the core microbial community in Italian Riesling wine fermentation consists of one non-Saccharomyces (S. bacillaris) and three S. cerevisiae strains (SC1, SC21, SC23). The synthetic microbial community under investigation in this study enables more precise identification of different S. cerevisiae genotypes, thus distinguishing it from conventional synthetic microbial communities. Accurate identification and utilization of these core microbes can provide the wine industry with an innovative fermentation strategy, thereby enhancing product flavor complexity and market competitiveness.
3.5. Fermentation performance and aroma of synthetic microbial communities
The present study focused on constructing and analyzing a synthetic microbial community for Italian Riesling wine, with the aim of closely replicating the chemical aroma profile of traditional spontaneous fermentation by controlling the mixture of core microbial species and the intraspecific diversity of S. cerevisiae. The subsequent section of this study involved an assessment of the effects of a synthetic community composed of S. bacillaris and S. cerevisiae SC1, SC21, and SC23. As shown in Fig. 5, the fermentation performance of the synthetic microbial consortia is demonstrated as follows: Except for the SB group, all other synthetic microbial consortia groups and their corresponding single-strain controls completed the fermentation process within 10 days without encountering fermentation stagnation or delays. This indicates the well-designed synthetic microbial consortia exhibit good rationality. Analyzing glycerol yield (Fig. 5B), the commercial yeast F15 showed the lowest glycerol production, while All-△SC23 and All-△SC21 exhibited the highest glycerol yields, followed by All-△SC1 and All, which were significantly higher than those of single-strain fermentations. This suggests that the synergistic action of the synthetic microbial consortia effectively enhances glycerol generation. Regarding ethanol content (Fig. 5C), the SB group, which did not complete fermentation, showed the lowest ethanol level. The commercial yeast F15 displayed the highest ethanol content, indicating its high efficiency in ethanol conversion. The ethanol levels of SC21 and SC23 were intermediate, with All falling in between. In terms of acetic acid production (Fig. 5D), the SB group exhibited the highest yield, followed by SC1. The acetic acid production of All-△SB and All-△SC23 was slightly higher than that of the All group.
Fig. 5.
Fermentation performance of core microbial strains. (A) Fermentation curve; (B) Glycerol; (C) Ethanol; (D) Acetic Acid.
PCA was employed to analyze key aroma compounds in wines produced by All, SF, community minus one strain, and single strain of Italian Riesling grapes. The results indicated that the PC1 and the PC2 of the PCA model explained 51.09 % and 17.32 % of the variance, respectively (Fig. 6A). It is noteworthy that the distance between the SF group and the All group was relatively small, indicating minor feature differences in the original high-dimensional space, consistent with the results reported by Peng et al. (2025). Additionally, hierarchical clustering analysis of key flavor compounds demonstrated that SF and All treatment groups formed a single cluster branch, confirming the absence of significant compositional divergence between these groups (Fig. 6B). These findings suggest that precise control of core microbial species and their intraspecific diversity can effectively mimic the key aroma chemical profiles of spontaneous fermentation, thereby providing the wine industry with an innovative fermentation strategy. In single-strain fermentations, SC23 demonstrated a marked promotion ability for the synthesis of ethyl acetate, 2-methoxy-4-ethylphenol, and isobutyric acid. SC1 exhibited high efficiency in the production of 2-methoxy-4-ethylphenol, while SC21 showed exceptional performance in the synthesis of 1-propanol. SB strains, on the other hand, displayed a clear advantage in the generation of phenol, phenethyl alcohol, and ethyl hexanoate. However, the fermentation characteristics of synthetic microbial communities are not merely the simple summation of the functional contributions of their constituent strains. These microorganisms form a complex network of interactions during fermentation, encompassing various ecological relationships such as mutualism, competition, antagonism, and metabolic cross-feeding. Through carefully designed species combinations, members of synthetic communities can establish mutually beneficial symbiotic mechanisms, such as metabolic cross-feeding, enabling them to collaboratively complete complex metabolic pathways that individual strains cannot achieve independently. This results in a significant enhancement of the synthetic capacity for specific flavor compounds. This knowledge gap constitutes a core bottleneck in this research field, constraining effective quality control and the achievement of industrialized production. Importantly, the present work is confined to laboratory scale, and scaling-up its conclusions to industrial fermenters remains a pivotal hurdle. Hence, forthcoming investigations will leverage transcriptomics to unravel the molecular basis of strain–strain interactions. Deciphering these mechanisms will furnish indispensable theoretical foundations and practical directives for advancing the controllability and consistency of industrial-scale Italian Riesling vinification. In summary, this study successfully constructed a synthetic microbial community whose fermentation product closely resembled the target Italian Riesling wine in terms of key aroma compound composition, odor activity values (OAV), and multivariate statistical models. This indicates that the synthetic community possesses the chemical foundation necessary to reproduce the target aroma profile. However, this similarity requires further confirmation through future sensory analyses, such as descriptive analysis and triangle tests.
Fig. 6.
Analysis of characteristics of Italian Riesling wine fermented with synthetic microbial community. (A) PCA analysis of key aroma compounds in Italian Riesling wine fermented with synthetic microbial community; (B) Analysis of key aroma compounds in Italian Riesling wine fermented with synthetic microbial community.
It should be noted that the conclusions of this study are primarily based on inferences from chemical data. Although OAV and multivariate statistical analyses are valuable tools for predicting sensory contributions, the absence of formal sensory evaluation—such as tests by a trained panel, recombination, or omission studies—represents a limitation of this work. Therefore, the current findings should be interpreted as achieving a chemical profile approaching that of the target aroma. Validating the actual sensory similarity remains a key objective for future research.
4. Conclusion
Fermented foods are indispensable components of our daily diet, and the regulation of fermentation processes to cater to the diverse dietary preferences of consumers is of paramount importance. This study employed a range of molecular biology techniques, including high-throughput sequencing, culturomics identification, and Interdelta PCR detection, to elucidate the spatiotemporal succession patterns of fungal communities and S. cerevisiae genotypes during the spontaneous fermentation of Italian Riesling wine grapes. Utilizing HS-SPME-GC–MS and OAV, 16 aroma compounds were confirmed as key contributors to the aroma profile of Italian Riesling wine. A correlation analysis was conducted between microbial communities, S. cerevisiae genotypes, and key aroma compounds. This analysis enabled the identification of four core microbial strains. The Saccharomyces strains under consideration are S. bacillari and S. cerevisiae (designated as SC1, SC21, and SC23). This is the first time that a synthetic microbial community has been constructed based on the intraspecific diversity of S. cerevisiae and utilized for the fermentation of Italian Riesling wine. Fermentation experiments confirmed that the synthetic community could effectively replicate the key aroma of Italian Riesling wine at the chemical level, thereby underscoring the critical role of these strains in flavor formation and providing novel solutions for quality control and flavor optimization in fermented foods.
CRediT authorship contribution statement
Xue Zhang: Writing – review & editing, Writing – original draft, Visualization, Methodology, Data curation. Tianyuan Zhang: Investigation. Yaoyao Song: Data curation. Yi Qin: Supervision. Yuyang Song: Supervision. Zhengwen Zhang: Data curation. Xingkai Liu: Data curation. Jiao Jiang: Project administration. Yanlin Liu: Resources, Project administration, Funding acquisition.
Declaration of competing interest
The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
Acknowledgements
This work was supported by Project supported by the Joint Funds of the National Natural Science Foundation of China (U21A20269), the Nation Natural Science Foundation of China (32372312), and the Agriculture Research System of China of MOF and MARA (CARS-29-jg-03). We are grateful to Professor Liang Yan Ying, laboratory administrator at the College of Enology, Northwest A&F University, Yangling, China, for her technical assistance in GC–MS analysis.
Footnotes
Supplementary data to this article can be found online at https://doi.org/10.1016/j.fochx.2025.103146.
Contributor Information
Yaoyao Song, Email: [email protected].
Yi Qin, Email: [email protected].
Yuyang Song, Email: [email protected].
Zhengwen Zhang, Email: [email protected].
Jiao Jiang, Email: [email protected].
Yanlin Liu, Email: [email protected].
Appendix A. Supplementary data
Data availability
The data that has been used is confidential.
References
- Boynton P.J., Greig D. Species richness influences wine ecosystem function through a dominant species. Fungal Ecology. 2016;22:61–72. doi: 10.1016/j.funeco.2016.04.008. [DOI] [Google Scholar]
- Chen K., Liu C., Wang Y., Wang Z., Li F., Ma L., Li J. Predominance of indigenous non-Saccharomyces yeasts in the traditional fermentation of greengage wine and their significant contribution to the evolution of terpenes and ethyl esters. Food Research International. 2021;143 doi: 10.1016/j.foodres.2021.110253. [DOI] [PubMed] [Google Scholar]
- Chen Y., Lei X., Wu Q., Qin Y., Song Y., Liu Y. Oenological suitability of Chinese indigenous Saccharomyces cerevisiae in chardonnay wine: The observation of grape maturity and vintage. Food Bioscience. 2024;61 doi: 10.1016/j.fbio.2024.104904. [DOI] [Google Scholar]
- Childs B.C., Bohlscheid J.C., Edwards C.G. Impact of available nitrogen and sugar concentration in musts on alcoholic fermentation and subsequent wine spoilage by Brettanomyces bruxellensis. Food Microbiology. 2015;46:604–609. doi: 10.1016/j.fm.2014.10.006. [DOI] [PubMed] [Google Scholar]
- Christofi S., Papanikolaou S., Dimopoulou M., Terpou A., Cioroiu B., Cotea V., Kallithraka S. Effect of yeast assimilable nitrogen content on fermentation kinetics, wine chemical composition and sensory character in the production of Assyrtiko wines. Applied Sciences. 2022;12:1405. doi: 10.3390/app12031405. [DOI] [Google Scholar]
- Cosetta C.M., Wolfe B.E. Deconstructing and reconstructing cheese rind microbiomes for experiments in microbial ecology and evolution. Current Protocols in Microbiology. 2020;56 doi: 10.1002/cpmc.95. [DOI] [PubMed] [Google Scholar]
- De Roy K., Marzorati M., Van den Abbeele P., Van de Wiele T., Boon N. Synthetic microbial ecosystems: An exciting tool to understand and apply microbial communities. Environmental Microbiology. 2014;16:1472–1481. doi: 10.1111/1462-2920.12343. [DOI] [PubMed] [Google Scholar]
- Det-Udom R., Gilbert C., Liu L., Prakitchaiwattana C., Ellis T., Ledesma-Amaro R. Towards semi-synthetic microbial communities: Enhancing soy sauce fermentation properties in B. subtilis co-cultures. Microbial Cell Factories. 2019;18:101. doi: 10.1186/s12934-019-1149-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Ding Y., Wang L., Gao Y., Zhang Z., Song Y., Wang H., Li H. Microbial succession during spontaneous fermentation of Ecolly grapes and their important contribution to flavor metabolites. Food Bioscience. 2024;62 doi: 10.1016/j.fbio.2024.105149. [DOI] [Google Scholar]
- Divol B., du Toit M., Duckitt E. Surviving in the presence of Sulphur dioxide: Strategies developed by wine yeasts. Applied Microbiology and Biotechnology. 2012;95:601–613. doi: 10.1007/s00253-012-4186-x. [DOI] [PubMed] [Google Scholar]
- Du R., Jiang J., Qu G., Wu Q., Xu Y. Directionally controlling flavor compound profile based on the structure of synthetic microbial community in Chinese liquor fermentation. Food Microbiology. 2023;114 doi: 10.1016/j.fm.2023.104305. [DOI] [PubMed] [Google Scholar]
- Dzialo M.C., Park R., Steensels J., Lievens B., Verstrepen K.J. Physiology, ecology and industrial applications of aroma formation in yeast. FEMS Microbiology Reviews. 2017;41:S95–S128. doi: 10.1093/femsre/fux031. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Gao J., Wu T., Geng H., Chai R., Huang W., You Y., Zhan J. Elucidating the relationship between microbial communities and the formation of flavour metabolites in cabernet sauvignon wine through metagenomic analysis. LWT-Food Science and Technology. 2024;213 doi: 10.1016/j.lwt.2024.117076. [DOI] [Google Scholar]
- González M.L., Chimeno S.V., Sturm M.E., Becerra L.M., Lerena M.C., Rojo M.C.…Mercado L.A. Populations of Saccharomyces cerevisiae in vineyards: Biodiversity and persistence associated with terroir. Fermentation. 2023;9:292. doi: 10.3390/fermentation9030292. [DOI] [Google Scholar]
- Großkopf T., Soyer O.S. Synthetic microbial communities. Current Opinion in Microbiology. 2014;18:72–77. doi: 10.1016/j.mib.2014.02.002. [DOI] [PMC free article] [PubMed] [Google Scholar]
- He X., Liu H., Lv C., Wang F., Zhao C., Tao R., Li J., Liu Z., Du L. Analysis of rice microbial communities under different storage conditions using culture-dependent and -independent techniques. Quality Assurance & Safety of Crops and Food. 2022;14:1–11. doi: 10.15586/qas.v14i1.993. [DOI] [Google Scholar]
- He Y., Wang X., Li P., Lv Y., Nan H., Wen L., Wang Z. Research progress of wine aroma components: A critical review. Food Chemistry. 2023;402 doi: 10.1016/j.foodchem.2022.134491. [DOI] [PubMed] [Google Scholar]
- Huang D., Zhong Y., Liu Y., Song Y., Zhao X., Qin Y. Reducing higher alcohols by integrating indigenous Saccharomyces cerevisiae, nitrogen compensation, and chaptalization methods during fermentation of kiwifruit wine. LWT-Food Science and Technology. 2023;184 doi: 10.1016/j.lwt.2023.115059. [DOI] [Google Scholar]
- Jia Y., Niu C., Lu Z., Zhang X., Chai L., Shi J., Xu Z., Li Q. A bottom-up approach to develop a synthetic microbial community model: Application for efficient reduced-salt broad bean paste fermentation. Applied and Environmental Microbiology. 2020;86 doi: 10.1128/AEM.00306-20. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Jiao J., Xia Y., Yang M., Zheng J., Liu Y., Cao Z. Differences in grape-surface yeast populations significantly influence the melatonin level of wine in spontaneous fermentation. LWT-Food Science and Technology. 2022;163 doi: 10.1016/j.lwt.2022.113568. [DOI] [Google Scholar]
- Jing J., Garbeva P., Raaijmakers J.M., Medema M.H. Strategies for tailoring functional microbial synthetic communities. The ISME Journal. 2024;18 doi: 10.1093/ismejo/wrae049. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lai Y., Yuan J., Chen Z., Wang D., Sun J., Ma J. Microwave irradiation: Reduction of higher alcohols in wine and the effect mechanism by employing model wine. LWT-Food Science and Technology. 2023;181 doi: 10.1016/j.lwt.2023.114765. [DOI] [Google Scholar]
- Li L., Li N., Fu J., Liu J., Ping Wen X., Cao H., Xu H., Zhang Y., Cao R. Synthesis of an autochthonous microbial community by analyzing the core microorganisms responsible for the critical flavor of bran vinegar. Food Research International. 2024;175 doi: 10.1016/j.foodres.2023.113742. [DOI] [PubMed] [Google Scholar]
- Liu Q., Zhao X., Jiang Z., Han X., Peng S., Wang J. Co-evolutionary dynamics of microbial communities and flavor profiles during natural fermentation of cabernet sauvignon and merlot: A comparative study within a single vineyard. Food Research International. 2025;200 doi: 10.1016/j.foodres.2024.115517. [DOI] [PubMed] [Google Scholar]
- Liu S., Lou Y., Li Y., Zhao Y., Laaksonen O., Li P., Zhang J., Battino M., Yang B., Gu Q. Aroma characteristics of volatile compounds brought by variations in microbes in winemaking. Food Chemistry. 2023;420 doi: 10.1016/j.foodchem.2023.136075. [DOI] [PubMed] [Google Scholar]
- Lu Y., Tan X., Lv Y., Yang G., Chi Y., He Q. Physicochemical properties and microbial community dynamics during Chinese horse bean-chili-paste fermentation, revealed by culture-dependent and culture-independent approaches. Food Microbiology. 2020;85 doi: 10.1016/j.fm.2019.103309. [DOI] [PubMed] [Google Scholar]
- Ma W., Yu J., Yang F., Zhang X., Zhang F., Jin W., Sun Z., Zhao Z., Jia S., Zhong C., Xue J. Metagenomic analysis of the relationship between the microorganisms and the volatiles' development in the wines during spontaneous fermentation from the eastern foothills of the Ningxia Helan mountains in China. Journal of the Science of Food and Agriculture. 2023;103:6429–6439. doi: 10.1002/jsfa.12718. [DOI] [PubMed] [Google Scholar]
- Ma Y., Peng S., Mi L., Li M., Jiang Z., Wang J. Correlation between fungi and volatile compounds during different fermentation modes at the industrial scale of merlot wines. Food Research International. 2023;174 doi: 10.1016/j.foodres.2023.113638. [DOI] [PubMed] [Google Scholar]
- McCarty N.S., Ledesma-Amaro R. Synthetic biology tools to engineer microbial communities for biotechnology. Trends in Biotechnology. 2019;37:181–197. doi: 10.1016/j.tibtech.2018.11.002. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Peng Q., Zheng H., Quan L., Li S., Huang J., Li J., Xie G. Development of a flavor-oriented synthetic microbial community for pour-over rice wine: A comprehensive microbial community analysis. Food Microbiology. 2025;126 doi: 10.1016/j.fm.2024.104677. [DOI] [PubMed] [Google Scholar]
- Peng Q., Zheng H., Zhou H., Chen J., Xu Y., Wang Z., Xie G. Elucidating core microbiota in yellow wine (Huangjiu) through flavor-oriented synthesis and construction of microbial communities. Food Research International. 2024;197 doi: 10.1016/j.foodres.2024.115139. [DOI] [PubMed] [Google Scholar]
- Romano P., Braschi G., Siesto G., Patrignani F., Lanciotti R. Role of yeasts on the sensory component of wines. Foods. 2022;11, Article 13 doi: 10.3390/foods11131921. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Sabach O., Buhnik-Rosenblau K., Kesten I., Freilich S., Freilich S., Kashi Y. The rise of the sourdough: Genome-scale metabolic modeling-based approach to design sourdough starter communities with tailored-made properties. International Journal of Food Microbiology. 2023;407 doi: 10.1016/j.ijfoodmicro.2023.110402. [DOI] [PubMed] [Google Scholar]
- Sun Y., Li E., Qi X., Liu Y. Changes of diversity and population of yeasts during the fermentations by pure and mixed inoculation of Saccharomyces cerevisiae strains. Annals of Microbiology. 2015;65, Article 2 doi: 10.1007/s13213-014-0934-8. [DOI] [Google Scholar]
- Tian S., Zeng W., Fang F., Zhou J., Du G. The microbiome of Chinese rice wine (Huangjiu) Current Research in Food Science. 2022;5:325–335. doi: 10.1016/j.crfs.2022.01.007. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Tlais A.Z.A., Kanwal S., Filannino P., Acin Albiac M., Gobbetti M., Di Cagno R. Effect of sequential or ternary starters-assisted fermentation on the phenolic and glucosinolate profiles of sauerkraut in comparison with spontaneous fermentation. Food Research International. 2022;156 doi: 10.1016/j.foodres.2022.111116. [DOI] [PubMed] [Google Scholar]
- Wang F., Zhu L., Hadiatullah H., Li Z., He J., Yao Y., Zhao G. Enhancing flavour with non-Saccharomyces during vinegar alcoholisation: A mechanism study. International Journal of Food Science and Technology. 2023;58:5001–5008. doi: 10.1111/ijfs.16584. [DOI] [Google Scholar]
- Wang L., Zhong X., Ding Y., Shao X., Zhang Z., Yin H., Zhang L., Wang H., Li H. Multi-omics co-analysis of the differences in microbial species composition and function between spontaneous and inoculated wine fermentation must. LWT-Food Science and Technology. 2024;200 doi: 10.1016/j.lwt.2024.116181. [DOI] [Google Scholar]
- Wei R., Chen N., Ding Y., Wang L., Liu Y., Gao F., Zhang L., Li H., Wang H. Correlations between microbiota with physicochemical properties and volatile compounds during the spontaneous fermentation of cabernet sauvignon (Vitis vinifera L.) wine. LWT-Food Science and Technology. 2022;163 doi: 10.1016/j.lwt.2022.113529. [DOI] [Google Scholar]
- Wei R., Ding Y., Chen N., Wang L., Gao F., Zhang L., Song R., Liu Y., Li H., Wang H. Diversity and dynamics of microbial communities during spontaneous fermentation of cabernet sauvignon (Vitis vinifera L.) from different regions of China and their relationship with the volatile components in the wine. Food Research International. 2022;156 doi: 10.1016/j.foodres.2022.111372. [DOI] [PubMed] [Google Scholar]
- Wu Q., Zhu Y., Fang C., Wijffels R.H., Xu Y. Can we control microbiota in spontaneous food fermentation? – Chinese liquor as a case example. Trends in Food Science & Technology. 2021;110:321–331. doi: 10.1016/j.tifs.2021.02.011. [DOI] [Google Scholar]
- Yan Y., Qian Y., Ji F., Chen J., Han B. Microbial composition during Chinese soy sauce koji-making based on culture dependent and independent methods. Food Microbiology. 2013;34:189–195. doi: 10.1016/j.fm.2012.12.009. [DOI] [PubMed] [Google Scholar]
- Zhang F., Tang Y., Ren Y., Yao K., He Q., Wan Y., Chi Y. Microbial composition of spoiled industrial-scale Sichuan paocai and characteristics of the microorganisms responsible for paocai spoilage. International Journal of Food Microbiology. 2018;275:32–38. doi: 10.1016/j.ijfoodmicro.2018.04.002. [DOI] [PubMed] [Google Scholar]
- Zhang X., Zhao X., Gao Y., Zhong X., Liang Y., Shao X.…Liu Y. Fungi diversity and volatile in spontaneously fermented Cabernet Sauvignon wines: Insights into four sub-regions Penglai’s Terroir. Food Bioscience. 2025;71:107049. doi: 10.1016/j.fbio.2025.107049. [DOI] [Google Scholar]
- Zhang X., Zhuang J., Wang X., Qin Y., Song Y., Liang Y.…Liu Y. Deterministic vs. stochastic: Fungal assembly driven by grape cultivar dictates divergent wine aromas in spontaneous fermentation. Food Research International. 2025;221:117473. doi: 10.1016/j.foodres.2025.117473. [DOI] [Google Scholar]
Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Supplementary Materials
Data Availability Statement
The data that has been used is confidential.






