The flavor formation and quality stability of solid-state fermented foods are closely linked to their storage process, and Chinese baijiu Daqu serves as an ideal model for studying such microecological succession. Analysis of Daqu produced in spring, autumn, and winter showed that despite seasonal differences in initial communities, all exhibited highly convergent succession during storage. Bacillaceae increased steadily, while Lactobacillaceae and Saccharomycetaceae declined. This restructuring corresponded with directional metabolic shifts: metabolites that decreased were enriched in amino acid pathways linked to the TCA cycle. Although amino acid levels declined, the metabolic potential for their utilization increased, while the abundances of core carbon metabolites and several TCA-related intermediates were relatively maintained during storage. Comparative genomic analysis further demonstrated that Bacillaceae MAGs possess a complete TCA cycle and abundant secondary metabolite clusters, whereas Lactobacillaceae lack a full TCA cycle, reflecting contrasting ecological strategies—Bacillaceae as stress-tolerant/homeostasis-maintaining and Lactobacillaceae as rapid-growth/resource-acquiring. Random forest analysis using three core families explained variation in key fermentation functions (cross-validated R2 = 0.504-0.787), supporting an association between microbial succession and Daqu performance. This work suggests that Daqu storage represents a directionally structured ecological succession associated with environmental variation, providing new insight into storage-stage ecological dynamics in solid-state fermentation.

Daqu serves as the saccharifying and fermenting starter in Baijiu production, yet the effects of raw material variation on community succession and metabolite formation during fermentation remain unclear. In this study, amplicon sequencing and metabolomic profiling were applied to compare mung bean Daqu (MBQ), produced by substituting pea with mung bean, with traditional medium-temperature Daqu. Microbial succession patterns were largely conserved after mung bean substitution, whereas stage-specific differences were observed in community composition, environmental associations, and microbial co-occurrence patterns. MBQ was enriched in thermotolerant spore-forming bacteria, particularly Kroppenstedtia, and functional fungi, including Thermomyces, Saccharomycopsis, and Aspergillus. These microbial differences were associated with higher saccharification, liquefaction, and fermentation powers at different stages. Spearman correlation analysis revealed distinct microbe-metabolite associations in MBQ involving pyrazines and plant-derived secondary metabolites. MBQ showed higher accumulation of higher alcohols during the middle stage, particularly phenylethyl alcohol (1.05-23.02 mg/kg), exclusive detection of 2,5-dimethylpyrazine and 2-ethylpyrazine, and flavonoid-related non-volatile metabolite profiles. These findings provide new insights into how raw material variation is associated with microbial succession and metabolic features during Daqu fermentation.

Microbial generalists are pivotal for maintaining the stability of fermentation systems, yet their distribution across different Baijiu types remains poorly understood. This study identified generalists and specialists during the pit fermentation of strong-flavor, jian-flavor, and sesame-flavor Baijiu in Anhui Province, and further elucidated their genomic features. Results showed that bacterial communities in all three types are dominated by generalists, whereas fungal communities depend more on diverse specialists. Bacterial generalists were represented by OTUs classified as Acetilactobacillus, Lactobacillus, and Limosilactobacillus. Targeted removal of these generalists increased the robustness of time-series networks, as they correlated negatively with most other taxa and were strongly linked to physicochemical properties. The major species belonging to bacterial generalists included Acetilactobacillus jinshanensis, Lactobacillus acetotolerans, and Limosilactobacillus pontis. These generalists possessed specialized genomic features for niche dominance, characterized by: (i) a low-acquisition, high-growth life history strategy (A/Y < 1); (ii) a preference for sugar metabolism (SAP >0); (iii) a complete multi-layered defense system conferring tolerance to acid and ethanol; and (iv) a streamlined (< 2 Mb) and non-redundant (lacking the TCA cycle) genome that minimizes regulatory burden. This study provides a systematic analysis of generalists across distinct Baijiu types in Anhui Province, offering a theoretical framework for understanding the rules of microbial assembly in the brewing process.

Natural exogenous additives (EA) suitable for the tobacco fermentation need to be developed to enhance the fermentation quality and economic value of low-grade cigar tobacco leaves (CTLs). This study analyzed the impacts of three compound Chinese herbal medicine (CHM) on metabolites and microorganisms during CTLs fermentation. The results manifested that EA facilitated the degradation of total sugar, starch and protein, while enhancing the accumulation of reducing sugar in CTLs. Furthermore, EA raised contents of free amino acids (FAAs), while Asp, Glu, Ser and His were found to be key differential FAAs of CTLs. During fermentation, the total contents of volatile flavor components (VFCs) initially increased and then declined. Furthermore, EA contributed to more harmonious compositions of VFCs by promoting the formation of neophytadiene, ketones, esters and aldehydes, as well as facilitating nicotine degradation. According to variable importance in the projection (VIP) > 1 and odor activity value (OAV) > 1, 7 key differential VFCs were identified. EA enhanced positive microbial interactions and led to a more stable and coordinated symbiotic network. Linear discriminant analysis effect size (LEfSe) identified 9 genera as differentially dominant microorganisms in CTLs, which were closely associated with chemical compositions and key differential flavor metabolites. In addition, EA promoted cigar tobacco characteristics (CTCs) by altering bacterial alpha diversity and influencing the assembly of dominant microbial communities. Overall, this study offered theoretical insights into the innovative applications of CHM in CTLs fermentation, and presented new perspectives for enhancing CTLs quality and customizing flavor profiles.

Biodegradation of lignite mediated by white-rot fungi has been reported by researchers, but the enzymatic mechanism of lignite is still unclear. The current study aims to see how the selected oxygen unit models found in lignite interact with laccase (Lac) from white-rot fungi with docking and molecular dynamics (MD) simulations. The results indicate that the number of key residues involved in Lac- PH–COOH were the largest and its H–bonds always existed during time. Both H–bond and hydrophobic interaction were important to maintain their binding. The Lac structure was the most stable when binding to PH–COOH, and the higher water molecules in binding region formed H–bond with PH–COOH. The optimal conditions were determined to be coal particle size of −0.2 mm, inoculated dosage of 10 mL, coal concentration of 0.9 g∙50 mL−1 and degradation time of 12d. The effect of parameters followed a decreasing order of coal particle size > inoculated dosage > coal concentration > degradation time. The mechanism degrading lignite was supposed: (1) Lac's T1 Cu2+ grabbed an electron from hydrogen on Ph–COOH, and a oxygen negative radical was formed causing breakage of C–C bond side chain. (2) The aromatic nitrogen positive radical was formed triggering its ring cleavage. This study provided the molecular basis for designing the enzyme to improve the lignite degradation.

Quorum sensing (QS) is a central system reflecting microbial collective behavior; however, its role in shaping functional microbial communities within complex solid-state fermentation matrices such as Daqu remains insufficiently understood. Here, we integrated amplicon sequencing, metagenomics, proteomics, and metabolomics to investigate autoinducer-2 (AI-2)-mediated quorum sensing dynamics during Daqu storage. Storage induced a directional succession of the microbial community, revealing two distinct ecological stages. The rapid adjustment stage (0-2 months) was characterized by strong homogeneous selection and rapid species turnover, whereas the slow stabilization stage (3-9 months) was dominated by gradual shifts in microbial relative abundances. Notably, the LuxS/AI-2 pathway, the only QS system detected during Daqu storage, declined rapidly and then stabilized, coinciding with the transition between the two ecological stages. During the early stage, the core QS protein LuxS was tightly associated with the dominant taxon Lactobacillaceae and the methyl donor S-adenosylmethionine, forming a synergistic functional module. In contrast, during the late stage, LuxS became decoupled from stress-tolerant taxa and showed weakened associations with resistance-related metabolic networks. This shift was accompanied by a metabolic transition, with carbon flux gradually redirected from active glycolysis toward the pentose phosphate pathway and amino acid biosynthesis during later stages. Collectively, these findings demonstrate that temporal modulation of the LuxS/AI-2 quorum sensing system represents a critical regulatory node reflecting the transition of the Daqu microbial community from cooperative growth to stress-resilient survival, ultimately shaping metabolic phenotypes and ecosystem functions during storage.

In order to deeply analyze the changing situation of nutrients during the fermentation of Dangshan pear juice by lactic acid bacteria, in this study, the ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) was used to analyze the metabolomics changes during the mixed fermentation of Dangshan pear juice by Lactobacillus plantarum and Lactobacillus acidophilus. The sensory evaluation results indicated that the fermented pear juice exhibited a better balanced sourness and sweetness, along with a more complex aroma profile. The principal component analysis (PCA) results indicated that all samples could be clearly classified into three categories. A total of 80 differential metabolites were identified through metabolomics analysis, mainly including amino acids, peptides, sugars and organic acids. The results by KEGG pathway enrichment analysis indicated that these differential metabolites were mainly involved in some key metabolic pathways such as phenylalanine, tyrosine and tryptophan metabolism, starch and sucrose metabolism, fructose and mannose metabolism, glutathione metabolism, arginine metabolism, as well as the tricarboxylic acid cycle and pyruvate metabolism. The research results showed that lactic acid bacteria fermentation could significantly change the composition of metabolites in pear juice, promoting the biodegradation of complex macromolecular substances, thereby improving its nutrition and functional properties. This study provides a theoretical basis and technical support for the industrial production of fermented beverages from Dangshan sweet pears.

This review comprehensively examines the structural architecture, catalytic mechanisms, and targeted molecular engineering of α-amylase (primarily the GH13 family), a pivotal biocatalyst in the food industry. We highlight diverse microbial sources of α-amylases and their cost-effective heterologous expression in well-characterized hosts like Bacillus subtilis and Escherichia coli. To overcome extreme operational bottlenecks—such as elevated temperatures and acidic environments—recent advances in protein engineering are critically evaluated. These strategies, including directed evolution, semi-rational design, and advanced immobilization on nanomaterials, synergistically enhance the enzyme’s thermostability, catalytic efficiency, and reusability. Furthermore, this paper synthesizes the state-of-the-art applications of engineered α-amylases across key food processing sectors, including baking, sugar refining, and brewing. By integrating structural biology with advanced material science, this review provides a targeted roadmap for developing next-generation, high-performance α-amylases to address current and future challenges in sustainable food processing.

Mung bean-flavor Baijiu (MBF) incorporates mung bean to develop a distinctive mung bean aroma (MBA), yet its key aroma compounds and formation mechanisms remain unclear. In this study, through aroma extract dilution analysis (AEDA), quantitative measurements, and aroma addition and omission, 22 key aroma compounds were identified that define the flavor profile of MBF. Among these, 2-isopropyl-3-methoxypyrazine, 1,1-diethoxy-3-methylbutane, 1-hexanol, furfural, furfuryl ethyl ether, and dimethyl trisulfide collectively shape the characteristic MBA. Furthermore, the integration of metabolic pathway analysis with amino acid and flavor profiling of the raw materials revealed that mung bean addition elevates the levels of linoleic acid, valine, leucine, and methionine, thereby promoting lipid oxidation, amino acid catabolism, and Maillard reactions that ultimately drive the formation of MBA compounds. These findings establish a molecular basis for MBA and advance the understanding of raw material driven regulation of characteristic aroma formation.

Agaricus bisporus is the most widely consumed edible mushroom and an important source of dietary protein and bioactive compounds. The casing layer plays a critical role in its cultivation, where microbial communities and metabolic activities strongly affect yield and quality, however, the stage-resolved research gap remains that it is still unclear which microbial and metabolic shifts in the casing layer are associated with primordia initiation and subsequent quality formation. In this study, the ecological and metabolic basis of mushroom quality formation was investigated by the combination of microbiome sequencing, non-targeted metabolomics, and functional genomics. Microbial communities exhibited stage-specific dynamics, with significant restructuring during primordia formation, when community cohesion and niche breadth reached their highest levels (0.68 +/- 0.06 and 4.48 +/- 1.05, respectively). A total of 1108 non-volatile metabolites were identified from metabolomic profiling. The adenosine and tryptophan exhibited significant changes and were enriched in energy and amino acid metabolism pathways. A representative strain, Pseudomonas putida AT130, was isolated from the genus Pseudomonas. The gene clusters related to phosphate solubilization, potassium mobilization, lignin degradation, and indole-3-acetic acid biosynthesis were revealed by genome analysis with the multifunctional activities being confirmed through in vitro assays. Pot experiments further showed that AT130 inoculation improved mushroom performance, increasing fruiting body yield by 123.55% and enhancing nutritional traits (protein and soluble sugars increased, whereas ash decreased) relative to the control. These findings linked casing-layer microbiota with mushroom quality and identified AT130 as a promising food-grade bioinoculant to enhance A. bisporus nutritional value and productivity.

The polycyclic aromatic hydrocarbons (PAH) degraded by bacterial laccase with the aid of 2, 2'-Azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) as mediator has been experimentally discovered by researchers, but its binding detail helping to deeply understand the enzymatic degradation process is still unclear. Here, the binding of low rank coal PAH, such as naphthalene (NAP), phenanthrene (PHE), anthracene (ANT) and pyrene (PYR), with ABTS mediated laccase were investigated with docking and molecular dynamics (MD). The results indicate that the number of hydrophobic interactions and key residues involved in laccase-PYR were the largest, and hydrophobic interaction were important to maintain their binding. The laccase was the most stable when it bound to PYR, and the water number in binding pocket maintained the minimal, which was difficult to form the hydration shell. The binding of PYR resulted in the quick folding of enzyme, and the water number in cavity increased to the largest to improve its solvent environment.

The quality, flavor, and stability of fermented foods depend on the microbial community. However, microbial dynamics are difficult to observe directly, leading to limited control over fermentation. High-throughput sequencing is a revolutionary tool for microbial characterization, among which DNA-based amplicon and metagenomic sequencing are core techniques. Nevertheless, the related data processing workflows in the context of fermented foods have not yet been systematically summarized, hindering the translation of research findings into fermentation practices. This review clarifies the applications of amplicon and metagenomic sequencing in fermented foods. For amplicon sequencing, the impacts of target regions, data preprocessing, and reference databases are addressed. For metagenomic sequencing, sequencing strategies, read-based and binning-based analytical methods, functional annotation, and species-specific databases are discussed. In addition, major strategies for downstream analysis of community data are summarized, including microbial diversity, co-occurrence networks, niche and community assembly, key environmental drivers, and machine learning-based prediction. Amplicon sequencing efficiently reveals microbial succession during fermentation but has limitations in functional annotation. Metagenomic sequencing is notable for functional annotation, enabling the linkage between microbial communities and metabolic potential alongside community characterization. Standardized data preprocessing and specific databases are critical for improving characterization. For community data, integrated analysis allows uncovering the driving factors of microbial succession, thereby helping to regulate fermentation. Notably, the compositional nature of the data must be considered and validated to avoid spurious associations. In summary, the exponential growth of sequencing data will propel the era of precision fermentation.

Daqu, a solid-state microbial starter for Baijiu, undergoes pronounced storage-driven ecological and functional shifts, yet how these changes functionally translate into downstream fermentation outcomes remains insufficiently understood. Here, we systematically tracked Daqu stored for 3, 6, and 9 months and evaluated its effects during controlled Zaopei fermentation. With increasing storage duration, the Daqu microbiota shifted from nutrient-sensitive taxa, including Saccharomycetaceae and Thermoascaceae, toward stress-tolerant groups such as Bacillaceae and Trichocomaceae. Concomitantly, functional potential transitioned from hexose metabolism and glycan biosynthesis toward amino acid metabolism and nucleotide-sugar biosynthesis, accompanied by a significant decline in the levels of 14 free amino acids. Fermentation experiments revealed that short-term stored Daqu promoted the migration of Mucoraceae and Enterobacteriaceae into Zaopei, enhanced saccharification and fermentation performance, and increased ester production, including ethyl E-2-hexenoate and ethyl 3-methylthiopropanoate. Conversely, nine-month stored Daqu favored the dominance of Bacillaceae and Trichocomaceae, intensified arginine and proline metabolism, accelerated amino acid turnover, and increased the formation of nitrogen-containing flavor compounds, notably pyrazines (2-ethyl-3,5-dimethylpyrazine; 2,3-diethylpyrazine). Collectively, these results demonstrate that Daqu storage functionally regulates fermentation performance and flavor formation through microbial and metabolic reprogramming, providing a basis for targeted flavor regulation in Baijiu and other solid-state fermented foods.

Dendrobium officinale flowers are valuable herbal materials with reported antioxidant and anti-inflammatory activities, but the microbial succession and metabolite transformation patterns during liquid fermentation remain insufficiently characterized. In this study, a mixed-culture fermentation system was established for D. officinale flowers, and the fermentation conditions were first optimized using DPPH free radical scavenging activity as the response index. Response surface methodology predicted a high-response condition of 32.8 °C, initial pH 3.93, and 6.16% sucrose, with a predicted DPPH scavenging rate of 0.858. Based on this condition, a 60-day dynamic fermentation experiment was conducted, and samples collected from JS10 to JS60 were analyzed by 16S rRNA sequencing, ITS sequencing, and untargeted LC-MS/MS metabolomics. Microbial community analysis showed a clear succession pattern during fermentation. The bacterial community was mainly composed of Lactiplantibacillus, Limosilactobacillus, and Lactobacillus, while the fungal community was dominated by Saccharomyces, with Papiliotrema showing a stage-dependent fluctuation and peaking at JS40. Metabolomics analysis identified 150 structurally annotated differential metabolites, and multivariate analysis indicated time-dependent changes in the metabolite profile. KEGG enrichment analysis highlighted pathways related to flavonoid biosynthesis, phenylpropanoid biosynthesis, flavone and flavonol biosynthesis, nucleotide metabolism, and ABC transporters. During prolonged fermentation, DPPH scavenging activity gradually decreased, whereas total amino acid content increased and total polysaccharides fluctuated. Several glycosides, nucleosides, phenylpropanoid/flavonoid-related metabolites, amino acids, and peptide-related compounds showed marked temporal changes. Spearman correlation analysis further suggested potential associations between dominant microbial taxa and key metabolite groups. Overall, this study shows that liquid fermentation of D. officinale flowers involves coordinated microbial succession and metabolite remodeling. These findings provide a multi-omics basis for understanding fermentation-associated biotransformation in Dendrobium flower materials.

Daqu is a key saccharifying and fermenting starter in Baijiu production. Mung bean Daqu (MBQ) is produced by replacing pea with mung bean in traditional medium-temperature Daqu, yet its functional characteristics remain unclear. This study integrated multi-omics approaches to investigate the effects of mung bean substitution on microbial community and functional expression in medium-temperature Daqu. MBQ retained dominant microbial genera, while Saccharopolyspora, Thermoactinomyces, Paecilomyces, and Aspergillus were identified as biomarkers. Following mung bean substitution, partial downregulation of α-amylase and significant upregulation of glucoamylase and β-fructofuranosidase reshaped starch degradation and promoted fermentable sugar release, while pyruvate conversion favored ethanol formation and reduced medium-chain fatty acid formation limited ester precursor availability. These changes were consistent with 25.38% and 117.78% increases in saccharifying and fermenting powers, respectively, along with lower liquefying and esterifying powers in MBQ. These findings provide new insight into raw material optimization for Daqu production.

Honey is a nutrient-rich natural functional food, with its color being considered as a key indicator of quality and consumer acceptance. Although various secondary metabolites are closely related to the color of honey, the specific substances and their exact effects on honey color remain unclear. In this study, the chemical composition, such as organic acids, polyphenols and vitamins, in different colored honey (Acacia, buckwheat, linden, vitex, lychee and jujube honey) were quantitatively analyzed using liquid chromatography-high resolution mass spectrometry (LCHRMS). The correlations between the chemical composition and the honey color were established by the mantel test. The results showed that quinic acid, ascorbic acid, and other composition were identified as significantly related with honey color. The validation experiments indicated that adding these significantly related substances to honey samples could multiplicatively deepen the honey color, and the value of the deepening color was positively correlated with that of the initial color. The study developed a practical and systematic LCHRMS method for analyzing chemical composition in honey. The results provided valuable scientific insights into the relationship between chemical composition and honey color. Additionally, it introduced a novel and feasible approach for investigating the effects of substances on the color of complex mixture systems.

The Chishui River is the prime production area for Jiang-flavor Baijiu in China, with 85

Kouzijiao (KZJ) is a traditional Jian flavor Baijiu (JFB) that exhibits flavor characteristics typical of both soy sauce flavor Baijiu (SSFB) and strong flavor Baijiu (SFB). However, the key aroma compounds and compositional changes during aging have not been clearly characterized, and manufacturers lack objective criteria to determine the optimal aging period for peak KZJ flavor. A total of 58 aroma compounds were identified in the KZJ from different years using a combined approach of headspace solid-phase microextraction (HS-SPME) and liquid--liquid extraction (LLE) coupled with gas chromatography-olfactometry (GC-O). There were 19 important aroma compounds (FD >= 9) with odor activity values (OAVs) >= 1 revealed by aroma extract dilution analysis (AEDA) and odor threshold calculations. Among them, ethyl 3-methylbutanoate and ethyl furfuryl ether were first identified as key aroma compounds in JFB. Recombination and omission experiments further confirmed that ethyl acetate, ethyl hexanoate, hexanoic acid, and dimethyl trisulfide made significant contributions to the characteristic aroma profile of KZJ. Moreover, one-way analysis of variance (ANOVA) showed that the levels of key aroma compounds remained relatively stable in KZJ3. This study provides critical insights into the quality control parameters and dynamic trends of key flavor compounds during the aging of KZJ.

Chinese Baijiu brewing relies on the vertical layering of Zaopei, yet its effect on microbial-flavor interactions remain unclear. This study employs result-oriented backward analysis of distinct flavor patterns to decipher how spatial differences govern metabolic networks and flavor distribution. GC-IMS/GC-MS revealed spatial divergence: the surface layer concentrated 62.89 % of total volatile flavors, significantly higher than the bottom layer (18.88 %) and the middle/upper layers (8.67-9.55 %). Fungal communities played a key role in layer differentiation (p = 0.002) through temperature and chemical changes. Deterministic selection dominated in hot and acidic (3.39 g/mol) surface layer (40.74 % |βNTI| > 2), while random drift prevailed in cool and high-ethanol (3.49 % v/v) bottom layer (NST = 78.14 %), with limited dispersal linking the layers. Five key flavor-related microbes were identified, highlighting the role of microbial metabolism in flavor development. Overall, the vertical structure of Zaopei guides the evolution of Baijiu's complex, multi-layered flavor profile.

The pyruvate dehydrogenase complex (PDHc) in Lactococcus lactis, composed of pdh E1α, E1β, and E2, links glycolysis to the tricarboxylic acid cycle (TCA cycle). This study investigated the effect of the pdh E2 knockout on metabolism. The knockout strain showed 76% biomass, 48% lower PDHc activity, and 13.4% reduced ATP versus wild type but a 1.5-fold higher NAD+/NADH ratio. Lactate production increased by 5.6% in the knockout and 45.3% in overexpressing strains. Next to this, the lactate dehydrogenase activity was induced, achieving the highest enzyme amount with the addition of 5 ng/mL nisin after 48 h of induction (28.7% higher than that of wild-type L. lactis). In addition, the transcript levels of genes related to the pyruvate metabolic pathway also changed: pdh E2 decreased by 67.62%, while pdh E1β was upregulated 15-fold. Our study provides insights for enhancing lactate production and understanding pdh E2 function.