Background Solid-state vinegar fermentation, predominantly practiced in China, is characterized by high microbial diversity, multi-substrate co-decomposition, abundant metabolite production, pronounced environmental heterogeneity, and complex interaction networks that collectively shape vinegar quality. However, this process remains largely experience-driven, with limited digitalization and an incomplete understanding of microbial interaction mechanisms. Key challenges include unclear interaction mechanisms, insufficient application of modeling tools such as genome-scale metabolic models, and limited capacity for dynamic process control. Addressing these gaps is essential for improving fermentation efficiency, stabilizing flavor quality, and advancing vinegar modernization. Scope and approach This review is centered on microbial interactions and outlines the metabolic division of labor of key microorganisms in solid-state fermentation and their roles in flavor formation. It examines microbial ecological relationships and interaction mechanisms, and analyzes how environmental heterogeneity regulates microbial interactions. The review further introduces synthetic microbial communities as tools for mechanism validation and functional reconstruction. Finally, based on clarified mechanisms, it discusses how key microbial, metabolic, and environmental information can be translated into model inputs to construct digital twin systems for directional control. Key findings and conclusions Environmental heterogeneity plays a role in shaping microbial interaction patterns, thereby influencing metabolic division of labor, fermentation efficiency, and flavor formation. Microbial interactions, rather than individual species, are drivers of community stability, functional metabolite production, and flavor complexity. The integrated application of synthetic microbial communities, metabolic flux models, and digital twin technologies constitutes a predictive framework for dissecting microbial interactions, optimizing key consortia, and achieving targeted regulation of cereal vinegar fermentation.

Microbial starters determine the quality of fermented shrimp products. Three rice wine lees starters (HSF, CZ, and AQ) were employed to ferment Pacific white shrimp under controlled conditions. The microbial community analysis indicated that HSF and CZ starters were dominated by Firmicutes or Ascomycota, with Pichia and Limosilactobacillus as the characteristic genera, whereas AQ was dominated by Mucoromycota, primarily Rhizopus. Fermentation with different rice wine lees significantly increased color values (L*, a*, and b*) and introduced more desirable volatile compounds. Total volatile contents varied markedly across fermented shrimps, ranked as HSF shrimp (236.41 μg/g) > CZ shrimp (178.60 μg/g) > AQ shrimp (87.27 μg/g). Correlation network model analysis further revealed that Firmicutes and Ascomycota exhibited significantly positive correlations with higher alcohols and esters, like 2-phenylethyl acetate and 2-phenylethanol. This study clarifies the microbial mechanisms underlying flavor formation and provides a theoretical basis for value-added fermented shrimp products.

Microbial communities serve as metabolic engines that determine the flavor and bioactivity of traditional fermented foods. Nonetheless, the stochastic nature of spontaneous fermentation often leads to niche uncertainty, resulting in inconsistent product quality and unstable functional expression. Transitioning traditional, empirically driven fermentation processes into precisely controllable modern biomanufacturing systems therefore requires an urgent paradigm shift from passive observation to active ecological engineering. In this review, we propose niche construction as a core strategy for the directional manipulation of microbial community assembly. We systematically examine the major dimensions of ecological niches in fermentation systems, including resource, environmental, spatial, and biotic niches, and further discuss how their temporal dynamics regulate microbial community assembly through dispersal, selection, ecological drift, and diversification. In addition, we assess specific engineering strategies based on niche construction, including the precise design of raw material substrates and the dynamic feedback regulation of fermentation parameters. Niche construction can reduce assembly stochasticity by guiding microorganisms from the occupation of available realized niches toward the expression of desired functional niches, thereby stabilizing flavor formation, bioactive metabolite production, and safety-related functions. Looking ahead, we explore the integration of artificial intelligence with multi-omics approaches for real-time niche prediction and the use of 3D printing to create spatially structured substrates, thereby enabling the precise manipulation of microbial spatial niches.

Eucommia ulmoides leaves, a traditional edible and medicinal resource, are a rich source of bioactive polyphenols. In this study, male Wistar rats served as the normal control, while spontaneously hypertensive rats were randomized into model, positive control (nifedipine, 6.0 mg/kg/d), and low-, medium-, and high-dose groups receiving 1.25, 2.50, and 3.75 mL/kg/d of the polyphenol extract (n = 8/group) via intragastric gavage for 4 weeks. The extract supplementation significantly reduced systolic and diastolic blood pressure to approximately 166.33 mmHg and 113.93 mmHg, respectively, thereby improving vascular function (p < 0.05), accompanied by alleviation of lipid metabolism disorders and oxidative stress. In addition, it mitigated intestinal injury and enhanced gut barrier integrity. Notably, it reshaped the gut microbiota by enriching beneficial bacteria and suppressing harmful taxa, which is associated with increased production of short-chain fatty acids. Integrated metabolomics analysis further demonstrated that it modulated multiple metabolic pathways, particularly arachidonic acid and tryptophan metabolism, which are closely linked to vascular homeostasis, inflammation, and oxidative stress. Collectively, these findings indicate that the antihypertensive effects of the polyphenol extract are potentially linked to the regulation of the gut microbiota–metabolite axis, highlighting its promising application as a functional food ingredient for cardiovascular health.

Chemical preservatives may pose safety concerns, while single-strain lactic acid bacteria often show limited antimicrobial efficacy due to nutritional dependence and restricted metabolic capacity. Here, we constructed antimicrobial synthetic consortia comprising lactic acid bacteria, yeast, and propionibacteria, optimized strain combinations by 96-well high-throughput screening, and investigated interspecific interactions using HPLC, qPCR, transcriptomics, and metabolomics. Results revealed that the optimal consortium, comprising Pediococcus acidilactici AAF5-2, Lactiplantibacillus plantarum C-35, and Wickerhamomyces anomalus 127, achieved an overall inhibition rate of 84.42%, calculated from its inhibitory effects against Escherichia coli ATCC 25922, Staphylococcus aureus ATCC 29213, Aspergillus niger CICC 2439, and Penicillium crustosum CICC 40656. It effectively promoted strain biomass accumulation, elevated glucose utilization efficiency, and shifted carbon metabolic flux to antimicrobial compound biosynthesis. Transcriptomic and metabolomic integration revealed a clear interspecific metabolic division of labor in the consortia: strain AAF5-2 undertook carbon capture and supply, strain C-35 specialized in antimicrobial substance biosynthesis, and strain 127 exerted cross-kingdom metabolic synergy, which jointly activated antimicrobial-related pathways and boosted overall antimicrobial activity. This study provides a food-grade high-efficiency antimicrobial synthetic microbial consortium, clarifies the interspecific interaction mechanism regulating antimicrobial function, and offers new strain resources and theoretical support for green biological preservation of fermented foods.

Solid-state fermentation (SSF) is a key process in biomanufacturing; however, surface-associated microbial growth, complex sample pretreatment, and signal interference caused by solid particles and complex matrices make it difficult to rapidly, continuously, and synchronously monitor microbial states and key metabolic indicators during fermentation, thereby hindering precise process control and intelligent production. To address this bottleneck, this study employed the SSF of Shanxi aged vinegar as a model system and developed a Process Analytical Technology (PAT) platform by integrating dielectrophoresis-assisted microfluidic single-cell Raman spectroscopy with machine learning, enabling the simultaneous analysis of microbial community composition and physicochemical indicators. a single-cell Raman spectral database was established, and 54 features were identified for six microbial biomarkers. Using a Logistic Regression model, the method achieved a classification accuracy of 99.6%, enabling effective tracking of microbial community succession. A Multilayer Perceptron algorithm was further employed to directly quantify key physicochemical indicators from complex process spectra, demonstrating excellent predictive performance for products acetic acid (R² = 0.93) and lactic acid (R² = 0.87), and subtract reducing sugars (R² = 0.87). This dual-dimensional PAT strategy was successfully validated in both a fermentation vats and the industrial closed solid-state fermenter, enabling synchronous feedback of microbial community dynamics and metabolic states within 1 hour. This rapid at-line monitoring approach bridges the gap between empirical observation and digital, rational process control, providing a robust data-driven foundation for the intelligent automation of complex solid-state biomanufacturing.

Cereal vinegars constitute a distinctive category across different vinegar varieties in the world. Among them, Shanxi aged vinegar (SAV) is characterized by distinct flavor and sensory profiles. This study aimed to explore the main skeleton aroma-active compounds (AAC) and sensory profiles of SAV. Similar aroma profiles of most SAV samples exhibited by E-nose and GC-MS. A total of 196 volatile compounds were identified in SAV. Among these, 46 compounds were designated as key AACs (odor activity value (OAV) ≥ 1). 35 compounds were identified as main skeleton AACs by multiple statistical analysis. Aldehydes and sulfur-compounds dominated the key AACs, with high OAVs for 3-methyl-butanal and methionol. The sensory wheel and main skeleton AACs of SAV were first assessed using check-all-that-apply (CATA) and OAV. The correlation between key AACs and sensory properties was analyzed, revealing that most of these compounds exert a significant influence on the sensory attributes of the vinegar.

The discrepancy between in situ microbial abundance and actual metabolic performance represents a critical challenge for interpreting microbial function from meta-omic data. Here, we integrated metagenomic and metatranscriptomic sequencing to investigate this decoupling between microbial abundance and cultivation-based physiological potential in Shanxi aged vinegar (SAV) solid-state fermentation. Lactobacillus acetotolerans dominated the community at both the genomic (40.89%) and transcriptomic (55.36%) levels, whereas Pediococcus acidilactici accounted for only 0.11%—a canonical rare-biosphere member. Source tracking via Sankey analysis showed that genes involved in acetate production were primarily attributed to Acetobacter pasteurianus, whereas genes involved in lactate production were predominantly associated with Lactobacillus spp. However, L. acetotolerans exhibited limited acid tolerance and lactic acid production, whereas the low-abundance P. acidilactici AAF1-5 displayed robust stress tolerance and superior lactic acid production under fermentation-relevant conditions—a striking contrast between microbial abundance and physiological performance. Metabolic interaction network analysis predicted that P. acidilactici may be co-inhibited by L. acetotolerans (Ixy = −2.737, resource competition) and A. pasteurianus (Ixy = −1.887, acid stress). To test whether ecological constraints, rather than intrinsic metabolic capacity, underlie this low abundance, we heterologously expressed the heat shock co-chaperone gene grpE from A. pasteurianus in P. acidilactici AAF1-5 as an experimental tool. The recombinant strain P. acidilactici-grpE exhibited significantly enhanced viability under acetic acid stress and, in simulated SAV fermentation, lactic acid content increased by 23.63% compared with the wild-type control. These results demonstrate that meta-omic abundance does not necessarily predict physiological performance and that low abundance may reflect ecological constraints rather than intrinsic functional deficiency. Our study provides an ecological framework for linking microbial abundance with physiological function beyond sequence-based abundance inference in complex fermentation microbiomes.

Aroma compounds in fermented foods are from raw material or produced by microorganisms, contributing to their diverse aroma profiles. The key odor-active compounds (OACs) present in Shanxi aged vinegar (SAV), one of China's famous vinegars, were systematically analyzed by molecular sensory science. A total of 152 OACs were identified in this study. Moreover, 87 OACs were quantitatively determined, and 37 OACs exhibited their odor activity values (OAVs) larger than 1. The aroma recombination and omission experiments confirmed that ketones, pyrazines, lactones, and acids are the most significant contributors to the aroma profiles of SAV. The correlation analysis confirmed that the absence of specific aroma compounds not only directly impacts the sensory characteristics associated with the missing compounds but also influences other sensory attributes. Therefore, 47 OACs, classified as key OACs through the verification of recombination and omission test, based on AEDA (FD ≥ 400) or OAV (≥1). Lastly, 6 aging-related markers (methional, 1-dodecanol, acetoin, benzyl acetate, propanoic acid, and trimethyl-pyrazine) were determined by machine learning based on key OACs. These results provide a standard for screening the key OACs that determine aroma characteristics of SAV, as well as for product quality control.

The changes of physiochemical properties, volatile and non-volatile metabolites across different stages of Monascus purpureus (M. purpureus) fermented surimi were systematically characterized. Pre-fermentation process led to a decrease in pH and a concurrent increase in color values and citrinin contents. Meanwhile, the total volatile basic nitrogen (TVB-N) levels increased gradually but maintained acceptable throughout the whole fermentation. GC-MS and E-nose results revealed that M. purpureus fermentation significantly enhanced surimi flavor profiles by accumulating esters and reducing aldehydes. The ester content reached 17.57 μg/g after 20 d of post-ripening process, representing 66.14% of the total volatile compounds. The pre-fermentation stage mainly involved enzyme-driven hydrolysis and formation of primary metabolites, whereas the post-ripening stage was characterized by the transformation of key intermediates and final flavor compounds. Collectively, the results provide a theoretical basis for targeted controlling the flavor formation of fermented surimi products.

Using 4-phenylbutan-2-one as the model substrate, an (R)-enantiospecific AmDH (M0) derived from l-amino acid dehydrogenase was converted into (S)-enantioselective enzymes (M4-M7) through several rounds of semirational iterative mutations. Variants M6-1 and M7 were successfully applied to synthesize (S)-amines (70-81% yields) and (R)-β-amino alcohols (60-65% yields) with 95% to >99% ee. Molecular dynamics simulations provided insights into the role of mutations in substrate recognition and stereoselective control, offering important guidance for regulating the stereoselectivity of AmDHs through protein engineering.

Melanoidins are brown macromolecular products of Maillard reaction formed through thermal processing, which provide unique flavor and bioactive function of food. This study aims to reveal the changes of structure and bioactive characteristics in beer melanoidin-rich fraction (BM) during different chemical treatments and in vitro digestion and fermentation. The results showed that BM had colloidal properties with 24.21-99.28 nm and negative charge, which mainly contained carbohydrates. In addition, microscopic morphology showed surface cracks after acid treatment, blocky particles after alkali treatment, and some porous small particles after salt treatment. These might be caused by the disruption of polysaccharide, protein, and the skeleton structure through spectra. Moreover, during simulated in vitro digestion stage, Mw of BM was slightly decreased, which might be due to the breakage of glycosidic bonds. Microscopic morphology presented a relatively complete block structure. However, the contents of total phenolics and flavonoids and the production of short-chain fatty acids were significantly increased during colonic fermentation process. Phloroglucinol was the main phenolic compound and its content also increased during colonic fermentation. Collectively, the results indicated that BM had relative stability during the digestion stage, and released bioactive compounds during colonic fermentation. These findings suggest that BM, as a novel colloidal prebiotic, possesses potential role in intestinal health.

Farnesoid X receptor (FXR) modulation represents a promising therapeutic strategy for metabolic dysfunction-associated steatohepatitis (MASH, formerly NASH); however, the development of MASH drugs from FXR full and partial agonists remains unsucessful. In this study, we employed ring cyclization of our previously identified chalcone FXR antagonists to homoisoflavonoid skeleton and to which attached various 7-ester and ether substituents. Among them, 4l was identified as most potent compound exhibiting high binding affinity and potent cellular antagonistic activity with an IC50 value of 0.70 μM. Molecular docking analysis revealed that the high affinity of 4l is driven by a T-shaped π-π stacking interaction and a robust hydrogen bond network within the FXR binding pocket. Further characterization revealed it functions as a highly selective FXR modulator by regulating the expression of downstream genes responsible for bile acid and lipid transporters (SHP, BSEP, SREBP-1c, and CYP7A1)-while sparing key gluconeogenic genes (PEPCK and G6Pase). In a CDA-HFD-induced MASH mouse model, oral administration of 4l significantly ameliorated hepatic steatosis, ballooning degeneration, and fibrosis, and dyslipidemia. Mechanistic studies further demonstrated that 4l exerts its lipid-lowering effects by activating the AMPK-ACC signaling pathway. Collectively, these findings highlight the 7-ether substituted homoisoflavonoid 4l as a novel, selective FXR modulator with significant therapeutic potential for the treatment of MASH.

Acetic acid fermentation (AAF) is a vital stage in the production of Shanxi aged vinegar (SAV), during which microbial community succession and metabolic reprogramming jointly determine acidification efficiency and flavor development. However, the system-level mechanisms linking microbial dynamics to functional metabolism during AAF remain insufficiently understood. In this study, metatranscriptomic analysis was employed combined with KEGG pathway enrichment, CAZy profiling, and global metabolic network visualization to elucidate the functional landscape of AAF across different fermentation stages. The results indicated a pronounced stage-dependent metabolic shift during AAF. In the early stage, nucleotide biosynthesis, and sugar metabolism pathways were highly active, accompanied by strong expression of CAZy-related genes, suggesting a growth-oriented metabolic strategy driven by efficient polysaccharide degradation and carbon assimilation. As fermentation progressed, mainly Acetobacter and Komagataeibacter, became functionally dominant, reinforcing nitrogen metabolism and central carbon metabolism. In the late stage, increasing acid stress induced a transition toward maintenance- and stress-adaptation-oriented metabolism, characterized by enhanced oxidative phosphorylation, ATP-dependent proton transport, nitrogen assimilation, and amino acid metabolism. Notably, amino acid metabolism emerged as a key metabolic axis linking stress tolerance and flavor maturation, while a clear functional division of labor between Lactobacillus and Acetobacter was observed, forming a cooperative metabolic network that stabilized fermentation performance. Collectively, this study provides a system-level view of microbial and metabolic coordination during SAV AAF and offers mechanistic insights into the self-organizing nature of solid-state vinegar fermentation.