Geographically Associated Fungus-Bacterium Interactions Contribute to the Formation of Geography-Dependent Flavor during High-Complexity Spontaneous Fermentation

Integrative metagenomics, volatilomics and chemometrics for deciphering the microbial structure and core metabolic network during Chinese rice wine (Huangjiu) fermentation in different regions

Huangjiu is a spontaneously fermented alcoholic beverage, that undergoes intricate microbial compositional changes. This study aimed to unravel the flavor and quality formation mechanisms based on the microbial metabolism of Huangjiu. Here, metagenome techniques, chemometrics analysis, and headspace solid-phase microextraction gas chromatography-mass spectrometry (HS-SPME-GC-MS) metabolomics combined with microbial metabolic network were employed to investigate the distinctions and relationship between the microbial profiles and the quality characteristics, flavor metabolites, functional metabolic patterns of Huangjiu across three regions. Significant variations (P < 0.05) were observed in metabolic rate of physicochemical parameters and biogenic amine concentration among three regions. 8 aroma compounds (phenethyl acetate, phenylethyl alcohol, isobutyl alcohol, ethyl octanoate, ethyl acetate, ethyl hexanoate, isoamyl alcohol, and diethyl succinate) out of 448 volatile compounds were identified as the regional chemical markers. 25 dominant microbial genera were observed through metagenomic analysis, and 13 species were confirmed as microbial markers in three regions. A metabolic network analysis revealed that Saccharomycetales (Saccharomyces), Lactobacillales (Lactobacillus, Weissella, and Leuconostoc), and Eurotiales (Aspergillus) were the predominant populations responsible for substrate, flavor (mainly esters and phenylethyl alcohol) metabolism, Lactobacillales and Enterobacterales were closely linked with biogenic amine. These findings provide scientific evidence for regional microbial contributions to geographical characteristics of Huangjiu, and perspectives for optimizing microbial function to promote Huangjiu quality.

Deciphering the core microbes and their interactions in spontaneous Baijiu fermentation: A comprehensive review

The spontaneous Baijiu fermentation system harbors a complex microbiome that is highly dynamic in time and space and varies depending on the Jiuqu starters and environmental factors. The intricate microbiota presents in the fermentation environment is responsible for carrying out various reactions. These reactions necessitate the interaction among the core microbes to influence the community function, ultimately shaping the distinct Baijiu styles through the process of spontaneous fermentation. Numerous studies have been conducted to enhance our understanding of the diversity, succession, and function of microbial communities with the aim of improving fermentation manipulation. However, a comprehensive and critical assessment of the core microbes and their interaction remains one of the significant challenges in the Baijiu fermentation industry. This paper focuses on the fermentation properties of core microbes. We discuss the state of the art of microbial traceability, highlighting the crucial role of environmental and starter microbiota in the Baijiu brewing microbiome. Also, we discuss the various interactions between microbes in the Baijiu production system and propose a potential conceptual framework that involves constructing predictive network models to simplify and quantify microbial interactions using co-culture models. This approach offers effective strategies for understanding the core microbes and their interactions, thus beneficial for the management of microbiota and the regulation of interactions in Baijiu fermentation processes.

Heterogenetic mechanism in high-temperature Daqu fermentation by traditional craft and mechanical craft: From microbial assembly patterns to metabolism phenotypes

The mechanical process has a widely usage in large-scale high-temperature Daqu (HTD) enterprises, however, the quality of the mechanical HTD is gapped with the HTD by traditional process. Currently, the understanding of the mechanism behind this phenomenon is still over-constrained. To this end, the discrepancies in fermentation parameters, enzymatic characteristics, microbial assembly and succession patterns, metabolic phenotypes were compared between traditional HTD and mechanical HTD in this paper. The results showed that mechanical process altered the temperature ramping procedure, resulting in a delayed appearance of the peak temperature. This alteration shifted the assembly pattern of the initial bacterial community from determinism to stochasticity, while having no impact on the stochastic assembly pattern of the fungal community. Concurrently, mechanical pressing impeded the accumulation of arginase, tetramethylpyrazine, trimethylpyrazine, 2-methoxy-4-vinylphenol, and butyric acid, as the target dissimilarities in metabolism between traditional HTD and mechanical HTD. Pearson correlation analysis combined with the functional prediction further demonstrated that Bacillus, Virgibacillus, Oceanobacillus, Kroppenstedtia, Lactobacillus, and Monascus were mainly contributors to metabolic variances. The Redundancy analysis (RDA) of fermented environmental factors on functional ASVs indicated that high temperature, high acid and low moisture were key positive drivers on the microbial metabolism for the characteristic flavor in HTD. Based on these results, heterogeneous mechanisms between traditional HTD and mechanical HTD were explored, and controllable metabolism targets were as possible strategies to improve the quality of mechanical HTD.

The mechanism of microbial structure and flavor characteristics in Qing-Jiang-flavor Jiupei regulated by different fermentation seasons

The physicochemical characteristics of Jiupei are crucial in regulating the metabolism of microbial communities and the flavor profile of Baijiu during the fermentation process. This study systematically monitored the physicochemical characteristics of Qing-Jiang-flavor Baijiu Jiupei (QJFJ) and analyzed its microbial community structure and flavor compounds. Results indicated that dominant bacteria were significantly enriched in Summer- and Autumn-Jiupei (Spring: Summer: Autumn: Winter = 1.00: 1.40: 1.29: 1.21), while dominant fungi were significantly enriched in Spring- and Autumn-Jiupei (Spring: Summer: Autumn: Winter = 1.45: 1.00: 1.35: 1.31). Sequentially, reducing sugars (day 0), temperature (day 5 - day 10), moisture (day 15), and acidity (day 20 - day 25) in Jiupei affected the succession pattern of the microbial community, regulating the abundance of Saccharomyces, Staphylococcus, Cyberlindnera, and Lactobacillus, individually. Alcohol and acid compounds are considered seasonal differential compounds in QJFJ. This study will provide a theoretical basis for Baijiu production across different seasons.

Selective Elucidation of Living Microbial Communities in Fermented Grains of Chinese Baijiu: Development of a Technique Integrating Propidium Monoazide Probe Pretreatment and Amplicon Sequencing

The fermentation process of Chinese Baijiu's fermented grains involves the intricate succession and metabolism of microbial communities, collectively shaping the Baijiu's quality. Understanding the composition and succession of these living microbial communities within fermented grains is crucial for comprehending fermentation and flavor formation mechanisms. However, conducting high-throughput analysis of living microbial communities within the complex microbial system of fermented grains poses significant challenges. Thus, this study addressed this challenge by devising a high-throughput analysis framework using light-flavor Baijiu as a model. This framework combined propidium monoazide (PMA) pretreatment technology with amplicon sequencing techniques. Optimal PMA treatment parameters, including a concentration of 50 μM and incubation in darkness for 5 min followed by an exposure incubation period of 5 min, were identified. Utilizing this protocol, viable microorganism biomass ranging from 8.71 × 106 to 1.47 × 108 copies/μL was successfully detected in fermented grain samples. Subsequent amplicon sequencing analysis revealed distinct microbial community structures between untreated and PMA-treated groups, with notable differences in relative abundance compositions, particularly in dominant species such as Lactobacillus, Bacillus, Pediococcus, Saccharomycopsis, Issatchenkia and Pichia, as identified by LEfSe analysis. The results of this study confirmed the efficacy of PMA-amplicon sequencing technology for analyzing living microbial communities in fermented grains and furnished a methodological framework for investigating living microbial communities in diverse traditional fermented foods. This technical framework holds considerable significance for advancing our understanding of the fermentation mechanisms intrinsic to traditional fermented foods.

Pediococcus spp.-mediated competition interaction within Daqu microbiota determines the temperature formation and metabolic profiles

Fermented microbiota is critical to the formation of microenvironment and metabolic profiles in spontaneous fermentation. Microorganisms generate a diverse array of metabolites concurrent with the release of heat energy. In the case of Daqu fermentation, the peak temperature exceeded 60°C, forming a typical high-temperature fermentation system known as high-temperature Daqu. However, microorganisms that cause the quality variation in Daqu and how they affect the functional microbiota and microenvironment in the fermentation process are not yet clear. This study adopted high-throughput sequencing and monitored the dynamic fluctuations of metabolites and environmental factors to identify the pivotal microorganism responsible for the alterations in interaction patterns of functional keystone taxa and quality decline in the fermentation system of different operational areas during the in situ fermentation process that had been mainly attributed to operational taxonomic unit (OTU)_22 (Pediococcus acidilactici). Additionally, we used isothermal microcalorimetry, plate inhibition experiments, and in vitro simulation fermentation experiments to explore the impact of Pediococcus spp. on heat generation, microorganisms, and metabolite profiles. Results showed the heat peak generated by Pediococcus spp. was significantly lower than that of Bacillus spp., filamentous fungi, and yeast. In addition, the preferential growth of P. acidilactici strain AA3 would obviously affect other strains to colonize through competition, and its metabolites made a significant impact on filamentous fungi. The addition of P. acidilactici strain AA3 in simulated fermentation would cause the loss of pyrazines and acids in metabolites. These evidences showed that the overgrowth of Pediococcus spp. greatly influenced the formation of high temperatures and compounds in solid-state fermentation systems. Our work illustrated the vital impact of interaction variability mediated by Pediococcus spp. for microbial assembly and metabolites, as well as in forming temperature. These results emphasized the functional role of Daqu microbiota in metabolites and heat production and the importance of cooperation in improving the fermentation quality.IMPORTANCEThe stable and high-quality saccharifying and fermenting starter in traditional solid-state fermentation was the prerequisite for liquor brewing. An imbalance of microbial homeostasis in fermentation can adversely impact production quality. Identification of such critical microorganisms and verifying their associations with other fermentation parameters pose a challenge in a traditional fermentation environment. To enhance the quality of spontaneous fermented products, strategies such as bioaugmentation or the control of harmful microorganisms would be employed. This work started with the differences in high-temperature Daqu metabolites to explore a series of functional microorganisms that could potentially contribute to product disparities, and found that the differences in interactions facilitated directly or indirectly by Pediococcus spp. seriously affected the development of microbial communities and metabolites, as well as the formation of the microenvironment. This study not only identified functional microbiota in Daqu that affected fermentation quality, but also demonstrated how microorganisms interact to affect the fermentation system, which would provide guidance for microbial supervision in the actual production process. Besides, the application of isothermal microcalorimetry in this study was helpful for us to understand the heat production capacity of microorganisms and their adaptability to the environment. This study presented a commendable framework for improving and controlling the quality of traditional fermentation and inspired further investigations in similar systems.

Using in situ untargeted flavoromics analysis to unravel the empty cup aroma of Jiangxiang-type Baijiu: A novel strategy for geographical origin traceability

"Empty cup aroma" is an important characteristic and quality evaluation standard of Jiangxiang-type Baijiu (JXB). In this study, an in situ detection method for the empty cup aroma of JXB was established, and the authenticity and origin information of JXB were identified with an untargeted flavoromics strategy. The complex composition of JXB leads to slow ethanol volatilization, which is a potential method for identifying artificial JXB. The results of the sensory analysis showed that acidic, sauce, burnt and qu in the empty cup of JXB were the strongest at the 45 min stage. A total of 155 compounds were detected in the empty cups of 15 JXB from different regions during 45 min of standing, and 34 compounds were identified as key aroma compounds in the empty cups of JXB. Eleven potential markers were screened (VIP > 1), which can be used to distinguish JXB produced in Guizhou/Sichuan and other regions.

Qu-omics elucidates the formation and spatio-temporal differentiation mechanism underlying the microecology of high temperature Daqu

Even if fermented in the same qu-room, Daqu will form various microecologies. A gradual differentiation of microbial population niches was observed within different qu-layers, manifesting as variations in the abundance of dominant microorganisms including Bacillus, Saccharopolyspora, Weissella, Kroppenstedtia, Thermoascus, Thermomyces, Saccharomycopsis, and Rasamsonia. Moreover, distinctions were observed in the functional expression of microorganisms, including Aspergillus, Virgibacillus, Oceanobacillus, and Neurospora. The community in middle layer Daqu exhibited characteristics of high compactness and niche diversity, which facilitated efficient substrate utilization. During the initial phase, the upper Daqu community demonstrated heightened activity. However, in the middle and lower layers, fungi and bacteria respectively exhibited greater functional expression. The key environmental factors regulating the assembly of communities in the upper and middle layers were pH and temperature, respectively, and the lower was moisture and acidity. Notably, deterministic assembly exerted a stronger influence on fungi.

Illuminating the Characteristics and Assembly of Prokaryotic Communities across a pH Gradient in Pit Muds for the Production of Chinese Strong-Flavor Baijiu

Pit mud (PM), as an important source of microorganisms, is necessary for Chinese strong-flavor baijiu (CSFB) production. Although it has been revealed that the PM prokaryotic community diversities are influenced by its quality, product area, ages, etc., the characteristics and assembly process of the prokaryotic community in PMs across a pH gradient are still unclear. In this study, the regular changes of α- and β-diversities of the prokaryotic community across a pH gradient in PMs were revealed, which could be divided into "stable", "relatively stable", and "drastically changed" periods. A total of 27 phyla, 53 classes, and 381 genera were observed in all given samples, dominated by Firmicutes, Bacteroidetes, Proteobacteria, Lactobacillus, Caproiciproducens, Proteiniphilum, etc. Meanwhile, the complexity of the network structure of the prokaryotic microbial communities is significantly influenced by pH. The community assembly was jointly shaped by deterministic and stochastic processes, with stochastic process contributing more. This study was a specialized report on elucidating the characteristics and assembly of PM prokaryotic communities across a pH gradient, and revealed that the diversity and structure of PM prokaryotic communities could be predictable, to some degree, which could contribute to expanding our understanding of prokaryotic communities in PM.

Temporal Profile of the Microbial Community and Volatile Compounds in the Third-Round Fermentation of Sauce-Flavor baijiu in the Beijing Region

Sauce-flavor baijiu produced in the Beijing and Guizhou regions has regional characteristic flavors, but the differences in flavor compounds and reasons for their formation remain unclear. The sauce-flavor baijiu brewing process involves several rounds of fermentation. In this study, we investigated the temporal distribution of microbial communities and flavor substances during the third round of sauce-flavor baijiu fermentation in the Beijing region, and we then compared and analyzed the differences of flavor substances and microorganisms in the fermented grains of sauce-flavor baijiu in the Beijing and Guizhou regions. It was found that 10 bacterial genera and 10 fungal genera were dominant in the fermented grains. The acidity of the fermented grains had a significant driving effect on the microbial community succession. A total of 81 volatile compounds were identified and quantified in the fermented grains, of which esters and alcohols were relatively abundant. The differences in 30 microbial community compositions and their resulting differences in terms of the fermentation parameters of fermented grains are responsible for the differences in the profiles of flavor compounds between sauce-flavor baijiu produced in the Beijing and Guizhou regions.

Airborne microorganisms and key environmental factors shaping their community patterns in the core production area of the Maotai-flavor Baijiu

Airborne microorganisms are important parts of the Moutai-flavor Baijiu brewing microbial community, which directly affects the quality of Baijiu. However, environmental factors usually shape airborne microbiomes in different distilleries, even in the different production areas of the same distillery. Unfortunately, current understanding of environmental factors shaping airborne microbiomes in distilleries is very limited. To bridge this gap, we compared airborne microbiomes in the Moutai-flavor Baijiu core production areas of different distilleries in the Chishui River Basin and systematically investigated the key environmental factors that shape the airborne microbiomes. The top abundant bacterial communities are mainly affiliated to the phyla Actinobacteriota, Firmicutes, and Proteobacteri, whereas Ascomycota and Basidiomycota are the predominant fungal communities. The Random Forest analysis indicated that the biomarkers in three distilleries are Saccharomonospora and Bacillus, Thermoactinomyces, Oceanobacillus, and Methylobacterium, which are the core functional flora contributing to the production of Daqu. The correlation and network analyses showed that the distillery age and environmental temperature have a strong regulatory effect on airborne microbiomes, suggesting that the fermentation environment has a domesticating effect on air microbiomes. Our findings will greatly help us understand the relationship between airborne microbiomes and environmental factors in distilleries and support the production of the high-quality Moutai-flavor Baijiu.

Predicting the final metabolic profile based on the succession-related microbiota during spontaneous fermentation of the starter for Chinese liquor making

Microbial inoculation is an effective way to improve the quality of fermented foods via affecting the microbiota structure. However, it is unclear how the inoculation regulates the microbiota structure, and it is still difficult to directionally control the microbiota function via the inoculation. In this work, using the spontaneous fermentation of the starter (Daqu) for Chinese liquor fermentation as a case, we inoculated different microbiota groups at different time points in Daqu fermentation, and analyzed the effect of the inoculation on the final metabolic profile of Daqu. The inoculated microbiota and inoculated time points both significantly affected the final metabolites via regulating the microbial succession (P < 0.001), and multiple inoculations can promote deterministic assembly. Twenty-seven genera were identified to be related to microbial succession, and drove the variation of 121 metabolites. We then constructed an elastic network model to predict the profile of these 121 metabolites based on the abundances of 27 succession-related genera in Daqu fermentation. Procrustes analysis showed that the model could accurately predict the metabolic abundances (average Spearman correlation coefficients >0.3). This work revealed the effect of inoculation on the microbiota succession and the metabolic profile. The established predicted model of metabolic profile would be beneficial for directionally improving the food quality.IMPORTANCEThis work revealed the importance of microbial succession to microbiota structure and metabolites. Multi-inoculations would promote deterministic assembly. It would facilitate the regulation of microbiota structure and metabolic profile. In addition, we established a model to predict final metabolites based on microbial genera related to microbial succession. This model was beneficial for optimizing the inoculation of the microbiota. This work would be helpful for controlling the spontaneous food fermentation and directionally improving the food quality.

Decoding temperature-driven microbial community changes and flavor regulation mechanism during winter fermentation of soy sauce

The flavor regulation of soy sauce fermented in winter is imminent challenge for the industry, while fermentation temperature is considered as an effective method to fortify soy sauce flavor. Thus, industrial-level fermentation systems with controlled temperature at 30°C (SSCT) and regular temperature (SSRT) in winter were designed to elucidate molecular basis and microbial regulatory mechanism of temperature-controlled flavor enhancement of soy sauce. Sensory evaluation suggested 30°C fermentation enhanced caramel-like, floral, fruity, roasted nut and smoky aroma. A total of 160 volatiles were identified, of which 39 components were evaluated for odor activity value (OAV). Eleven volatiles were determined as the odor markers distinguishing the aroma profiles of SSRT and SSCT, among which 2,5-dimethyl-4-hydroxy-3(2H)-furanone (HDMF, caramel-like), β-damascenone (floral), ethyl 2-methylpropanoate (fruity), ethyl acetate (fruity) and 2/3-methyl-1-butanol (malty, alcoholic) were largely responsible for the flavor enhancement. Moreover, high-throughput sequencing results demonstrated the temperature intervention induced more differential bacterial structure (R = 0.324, P = 0.001) than fungal structure (R = 0.069, P = 0.058). Correlation analysis revealed dominant and low-abundance genus together drove the formation and variation of volatile profile, particularly Weissella, Tetragenococcus, Starmerella and Pediococcus. Representatively, the formation pathways of key aroma substances HDMF and 5-ethyl-4-hydroxy-2-methyl-3(2H)-furanone (HEMF) were elaborated. Both temperature-mediated abiotic reactions and gene functions of microbiota were proposed to favor the yields of HDMF and C5 precursor of HEMF, whereas the small populations of Zygosaccharomyces and insufficient acetaldehyde limited the elevation of the HEMF level through the biosynthesis pathway. This study provided the practical and theoretical basis for the industrial applications of temperature control in soy sauce fermentation.

Integrated characterization of filler tobacco leaves: HS-SPME-GC-MS, E-nose, and microbiome analysis across different origins

This study delves into the aroma characteristics and microbial composition of filler tobacco leaves (FTLs) sourced from six distinct cigar-growing regions within Yunnan, China, following standardized fermentation. An integrated approach using gas chromatography-mass spectrometry (GC-MS), electronic nose (E-nose), and microbiome analysis was employed for comprehensive profiling. Results derived from Linear Discriminant Analysis (LDA) using E-nose data confirmed the presence of notable variability in flavor substance profiles among the FTLs from six regions. Additionally, GC-MS was used to discern disparities in volatile organic compound (VOC) distribution across FTLs from these regions, identifying 92, 81, 79, 58, 69, and 92 VOCs within each respective sample set. Significantly, 24 VOCs emerged as pivotal determinants contributing to the heterogeneity of flavor profiles among FTLs from diverse origins, as indicated by Variable Importance for the Projection (VIP) analysis. Furthermore, distinctions in free amino acid content and chemical constituents were observed across FTLs. Of noteworthy significance, solanone, isophorone, durene, (-)-alpha-terpineol, and 2,3'-bipyridine exhibited the strongest correlations with microbiome data, with fungal microorganisms exerting a more pronounced influence on metabolites, as elucidated through two-way orthogonal partial least-squares (O2PLS) modeling. These findings provide a theoretical and technical basis for accurately evaluating the synchronization of FTLs in aromas and fermentation processes, and they will enhance the quality of fermented FTLs and foster the growth of the domestic cigar tobacco industry ultimately.

Airborne microbes in five important regions of Chinese traditional distilled liquor (Baijiu) brewing: regional and seasonal variations

Baijiu is one of the six primary distilled spirits in the world. It is produced through the solid-state fermentation of grains in the open environment, so high-quality Baijiu brewing largely depends on terrior. Environmental microbes are one of the most important factors affecting the quality, quantity, and flavors of Baijiu. As atmosphere is a pool and transport pathway for microbes from the ambient environment to Baijiu brewing ecosystems, we explored the functional microbes of Baijiu brewing in five important regions. The regions fell into two topographical types, namely, plain and river-valley. In total, 41 functional microbes were identified rich (relative abundance >0.1%) in at least one of the regions, such as the fungi of Aspergillus, Candida, Cladosporium, Debaryomyces, Penicillium, Pichia, Rhizopus, Saccharomyces, and Wickerhamomyces and the bacteria of Acetobacter, Bacillus, Clostridium, Enterobacter, Lactobacillus, Methanosarcina, Methanobacterium, Methanobrevibacter, and Pseudomonas. However, some functional bacteria (e.g., Clostridia, Gluconacetobacter, and Weissella) and fungi (e.g., Dekkera, Eurotium, Issatchenkia, Mucor, and Phoma) were not rich or were not detected in the atmosphere. Airborne microbiomes and the Phylogenetic Diversity (PD) index were significantly different between the main brewing season (winter) and the summer break in each region, except for the fungi in one region. In winter, airborne microbiomes were significantly different among almost all the regions. The relative abundance of bacterial fermentation function in each region increased from summer to winter. The relative abundances of fungal yeast function were higher in winter for the plain regions but were higher in summer for the river-valley regions. In sum, our results suggested that: (1) atmosphere was one but not the sole important source of functional microbes for Baijiu brewing and (2) microbiomes in different regions might be quite different but they could share some major functions related to Baijiu brewing.

Comparison of the Correlations of Microbial Community and Volatile Compounds between Pit-Mud and Fermented Grains of Compound-Flavor Baijiu

The microbial composition and volatile components of fermented grains (FG) and pit mud (PM) are crucial for the quality and flavor of compound-flavor baijiu (CFB). The physicochemical indices, culturable microorganisms, microbial communities, and volatile components of FG and PM were analyzed and correlated in our research. Considering FG and PM, amplicon sequencing was used to analyze the microbial community and the volatile components were detected by headspace solid-phase microextraction-gas chromatography-mass spectrometry (HS-SPME). For FG, redundancy analysis and correlation perfume Circos were used to clarify the correlations between the dominant microbial community and volatile components. The results showed that Aspergillus, Pichia, and Rhizopus were the main fungal microflora in FG and PM, whereas Lactobacillus and Bacillus were the dominant bacteria in FG, and Methanosarcina and Clostridium sensu stricto 12 were the dominant bacteria in the PM. The microbial community and volatile compounds in the CB sampled from the bottom layers of the FG were greatly affected by those in the PM. There were 32 common volatile components in CB and PM. For FG, most of the volatile components were highly correlated with Lactobacillus, Bacillus, Aspergillus, Pichia, and Monascus, which includes alcohols, acids and esters. This study reveals correlations between microbial composition, volatile components, and the interplay of FG and PM, which are conducive to optimizing the fermentation process and improving the quality of CFB base.

Distribution, assembly, and interactions of soil microorganisms in the bright coniferous forest area of China's cold temperate zone

The bright coniferous forest area in the cold temperate zone of China is a terrestrial ecosystem primarily dominated by low mountain Larix gmelinii trees. Limited information is available regarding the assembly mechanisms and interactions of microbial communities in the soil in this region. This study employed high-throughput techniques to obtain DNA from myxomycetes, bacteria, and fungi in the soil, evaluated their diversity in conjunction with environmental factors, associated them with the assembly process, and explored the potential interaction relationships between these microorganisms. The findings of our study showed that environmental factors had a more significant influence on the α and β diversity of bacteria compared to myxomycetes and fungi. Microbial communities were influenced by environmental selection and geographical diffusion, although environmental selection appeared to have a more significant impact than geographical diffusion. Our study suggested that different microorganisms exhibited unique evolutionary patterns and may have different assembly modes within phylogenetic groups. Myxomycetes and fungi exhibited a similar assembly process that was mainly influenced by stochastic dispersal limitation and drift. In contrast, bacteria's assembly process was primarily influenced by stochastic drift and deterministic homogeneous selection. The community of myxomycetes and fungi is greatly influenced by spatial distribution and random events, while bacteria have a relatively stable population composition in specific regions and may also be subject to environmental constraints. Finally, this study revealed that Humicolopsis cephalosporioides, a fungus that exclusively resided in cold environments, may play a critical role as a keystone species in maintaining molecular ecological networks and was considered a core member of the microbiome.

Exploring the controllability of the Baijiu fermentation process with microbiota orientation

Product quality and stability improvement is important for development of the Baijiu industry. Generally, Baijiu brewing is carried out in a spontaneous fermentation system mediated by microbiota. Thus, complexity and instability are major features. Due to the insufficient understanding of the mechanism for producing Baijiu, the precise control of the fermentation progress has still not been realized, ultimately affecting product quality and stability. The flavor of Baijiu is the most important factor in determining its quality and is formed by microbiota under the driving force of various physicochemical parameters, such as moisture, acidity, and temperature. Therefore, exploring the association among microbiota (core), physicochemical factors (reference) and flavor compounds (target) has become a key point to clarify the formation mechanism for the flavor quality of Baijiu. Daqu fermentation and liquor fermentation are the two major stages of Baijiu brewing. Daqu, distillers' grains, and pit mud, as the most important fermentation substrates of the microbiota respectively, provide a large number of functional microorganisms related to the flavor components. To this end, we reviewed the relevant research progress of microbiota diversity in different fermentation substrates and the interaction mechanisms among microbiota, physicochemical parameters, and flavor components in this paper. Moreover, a research hypothesis of precise control of the Baijiu fermentation process by building fermentation models based on this is proposed. The key point for this idea is the identification of core microbiota closely associated with the formation of key flavor components by multi-omics technology and the acquisition of culturable strains. With this foundation, fermentation models suitable for different brewing environments will be established by constructing synthetic microbiota, designing mathematical models, and determining key fermentation model parameters. The ultimate goal will be to effectively improve the quality and stability of Baijiu products through model regulation.

Unravelling Metabolic Heterogeneity of Chinese Baijiu Fermentation in Age-Gradient Vessels

Fermentation vessels affect the characteristics of food fermentation; however, we lack an approach to identify the biomarkers indicating fermentation. In this study, we applied metabolomics and high-throughput sequencing analysis to reveal the dynamic of metabolites and microbial communities in age-gradient fermentation vessels for baijiu production. Furthermore, we identified 64 metabolites during fermentation, and 19 metabolites significantly varied among the three vessels (p < 0.05). Moreover, the formation of these 19 metabolites were positively correlated with the core microbiota (including Aspergillus, Saccharomyces, Lactobacillus, and Bacillus). In addition, ethyl lactate or ethyl acetate were identified as the biomarkers for indicating the metabolism among age-gradient fermentation vessels by BP-ANN (R2 > 0.40). Therefore, this study combined the biological analysis and predictive model to identify the biomarkers indicating metabolism in different fermentation vessels, and it also provides a potential approach to assess the profiling of food fermentations.

Directionally controlling flavor compound profile based on the structure of synthetic microbial community in Chinese liquor fermentation

Most traditional fermented foods are produced by spontaneous fermentation. It is difficult to produce traditional fermented foods with desired flavor compound profile. In this study, using Chinese liquor fermentation as a case, we aimed to directionally control flavor compound profile in food fermentation. Twenty key flavor compounds were identified in 80 Chinese liquor fermentations. Six microbial strains, identified as high producers of these key flavor compounds, were used to generate the minimal synthetic microbial community. A mathematical model was established to link the structure of the minimal synthetic microbial community and the profile of these key flavor compounds. This model could generate the optimal structure of synthetic microbial community to produce flavor compounds with desired profile. This work provided a strategy to realize the directional control of flavor compound profile via controlling the structure of the synthetic microbial community in Chinese liquor fermentation.

Spatiotemporal accumulation differences of volatile compounds and bacteria metabolizing pickle like odor compounds during stacking fermentation of Maotai-flavor baijiu

Pickle like odor (PLO) is undesirable in Maotai-flavor baijiu; however, its formation mechanism is unclear. Furthermore, there is a lack of understanding of the spatiotemporal accumulation of volatile compounds (including PLO compounds, PLOC) and of the microorganisms responsible for the production of PLOC during stacking fermentation. In this study, we analyzed the spatiotemporal distribution differences of 132 volatile compounds in piled fermented grains. PLOC (n = 5) were higher in pile surface than in pile center, reaching their highest levels at 6th and 5th rounds, respectively. The microorganisms in pile center were more conducive to the formation of alcohols, while those in the pile surface more promoted the synthesis of esters. Rhodococcus and Zygosaccharomyces promoted the formation of PLOC. Acetobacter was negatively correlated with the content of sulfur compounds by promoting their conversion into non-volatile sulfur compounds, thereby reducing the content of PLOC. This study provides information on the spatiotemporal differences of volatile compounds (especially PLOC) in piled fermented grains and identified the microorganisms that produce PLOC.

Applications of multi-omics techniques to unravel the fermentation process and the flavor formation mechanism in fermented foods

Fermented foods are important components of the human diet. There is increasing awareness of abundant nutritional and functional properties present in fermented foods that arise from the transformation of substrates by microbial communities. Thus, it is significant to unravel the microbial communities and mechanisms of characteristic flavor formation occurring during fermentation. There has been rapid development of high-throughput and other omics technologies, such as metaproteomics and metabolomics, and as a result, there is growing recognition of the importance of integrating these approaches. The successful applications of multi-omics approaches and bioinformatics analyses have provided a solid foundation for exploring the fermentation process. Compared with single-omics, multi-omics analyses more accurately delineate microbial and molecular features, thus they are more apt to reveal the mechanisms of fermentation. This review introduces fermented foods and an overview of single-omics technologies - including metagenomics, metatranscriptomics, metaproteomics, and metabolomics. We also discuss integrated multi-omics and bioinformatic analyses and their role in recent research progress related to fermented foods, as well as summarize the main potential pathways involved in certain fermented foods. In the future, multilayered analyses of multi-omics data should be conducted to enable better understanding of flavor formation mechanisms in fermented foods.

Revelation for the Influence Mechanism of Long-Chain Fatty Acid Ethyl Esters on the Baijiu Quality by Multicomponent Chemometrics Combined with Modern Flavor Sensomics

Long-chain fatty acid ethyl ester (LCFAEEs) is colorless and has a weak wax and cream aroma. It can be used as an intermediate for the synthesis of emulsifiers, and stabilizers and be applied in the production of flavor essence. It is also an important trace component in Baijiu and is attributed to making a contribution to the quality of Baijiu, but its distribution in Baijiu has not been clear, and its influence mechanisms on Baijiu quality have not been systematically studied. Therefore, the distribution of LCFAEEs for Baijiu in different years (2014, 2015, 2018, and 2022), different grades (premium, excellent, and level 1; note: here Baijiu grade classification was based on Chinese standard (GB/T 10781) and enterprise classification standard), and different sun exposure times (0, 6, 12, 20, 30, and 50 days) was uncovered. Thus, in this study, the effect of LCFAEEs on the quality of Baijiu was comprehensively and objectively proven by combining modern flavor sensomics and multicomponent chemometrics. The results showed that with the increase in Baijiu storage time, the concentration of LCFAEEs increased significantly in Baijiu (4.38–196.95 mg/L, p < 0.05). The concentration of LCFAEEs in level 1 Baijiu was significantly higher than that in excellent and premium Baijiu (the concentration ranges of ET, EP, EO, E9, E912, and E91215 were: 0.27–2.31 mg/L, 0.75–47.41 mg/L, 0.93–1.80 mg/L, 0.98–12.87 mg/L, 1.01–27.08 mg/L, and 1.00–1.75 mg/L, respectively, p < 0.05). With the increase in sun exposure time, the concentration of LCFAEEs in the Baijiu first increased significantly and then decreased significantly (4.38–5.95 mg/L, p < 0.05). As the flavor sensomics showed, the concentrations of LCFAEEs in Baijiu bodies were significantly correlated with the Baijiu taste sense (inlet taste, aroma sensation in the mouth), as well as with the evaluation after drinking (maintaining taste) (p < 0.05, r > 0.7). Based on the above, LCFAEEs are critical factors for Baijiu flavor thus, it is essential to explore a suitable concentration of LCFAEEs in Baijiu to make Baijiu’s quality more ideal.

Effect of Environmental Microorganisms on Fermentation Microbial Community of Sauce-Flavor baijiu

The compositions of the microbial community in fermented grains of Sauce-flavor baijiu produced in different regions have diverse characteristics; however, the reasons for this remain unclear. The present study investigated the contributions of environmental microorganisms to the microbial community as well as the volatile compounds in the fermented grains of Sauce-flavor baijiu produced in the Beijing region using high-throughput sequencing combined with sourcetracker analysis, and compared the differences of environmental microorganism and their roles in the production process of Sauce-flavor baijiu from different regions.The results showed that the environmental microorganisms in the tools were the main contributors of the bacterial and fungal communities in fermented grains during heap fermentation and at the beginning of pit fermentation. At the end of pit fermentation, pit mud was the main environmental source of bacterial community in fermented grains, while tools and Daqu were the main environmental sources of fungal community in fermented grains.Environmental microorganisms thrived on the functional microorganisms in the fermented grains of Sauce-flavor baijiu produced in the Beijing region and thus shaped the profiles of volatile compounds. Environmental microorganisms of Sauce-flavor baijiu in the Guizhou province and the Beijing region differed significantly, which is partially responsible for the distinctive characteristics in the microbial community structure of Sauce-flavor baijiu-fermented grains from different regions.

Systematic Review of Actinomycetes in the Baijiu Fermentation Microbiome

Actinomycetes (a group of filamentous bacteria) are the dominant microbial order in the Daqu (DQ) fermentation starter and in the pit mud (PM) of the Baijiu fermentation microbiome. Actinomycetes produce many of the key enzymes and flavor components, and supply important precursors, which have a major influence on its characteristic aroma components, to other microorganisms during fermentation. This paper reviews the current progress on actinomycete research related to Baijiu fermentation, including the isolation and identification, distribution, interspecies interactions, systems biology, and main metabolites. The main metabolites and applications of the actinomycetes during Baijiu fermentation are also discussed.