Insights into the bacterial, fungal, and phage communities and volatile profiles in different types of Daqu

Dynamic Changes and Potential Correlations between Microbial Diversity and Volatile Flavor Compounds in Chinese Medium-Temperature Daqu during Manufacturing

To investigate the dynamic changes and potential correlations between microbial diversity and volatile organic compounds (VOCs) during Chinese medium-temperature Daqu (MTD) manufacturing at different key stages, in this study, high-throughput sequencing (HTS) and gas chromatography-ion mobility spectrometry (GC-IMS) were employed to analyze the microbial diversity and VOCs of MTD, respectively. The results showed that Weissella, Staphylococcus, Thermoactinomyces, Kroppenstedtia, and Lactobacillus were the dominant bacterial genera, while Aspergillus, Alternaria, Thermoascus, Thermomyces, Wickerhamomyces, and Saccharomyces were the dominant fungal genera. A total of 61 VOCs were detected by GC-IMS, among which, 13 differential VOCs (VIP > 1) were identified, that could be used as potential biomarkers to judge the fermentation stage of MTD. Kroppenstedtia and Saccharopolyspora were positively correlated with 3-methyl-2-butenal and 2,2,4,6,6-pentamethylheptane-D, respectively, and both of these were positively correlated with butanal-D. Acetobacter, Streptomyces, and lactic acid bacteria (LAB) including Leuconostoc, Pediococcus, Weissella, and Lactobacillus were negatively correlated with their associated VOCs, while fungi were generally positively correlated with VOCs. Wickerhamomyces, Saccharomyces, and Candida were positively correlated with butan-2-one-M. This study provides a theoretical basis for explaining the mechanisms of MTD flavor formation and screening functional microorganisms to improve the quality of MTD.

Species-level understanding of the bacterial community in Daqu based on full-length 16S rRNA gene sequences

Daqu is used as the fermentation starter of Baijiu and contributes diversified functional microbes for saccharifying grains and converting sugars into ethanol and aroma components in Baijiu products. Daqu is mainly classified into three types, namely low (LTD), medium (MTD) and high (HTD) temperature Daqu, according to the highest temperatures reached in their fermentation processes. In this study, we used the PacBio small-molecule real-time (SMRT) sequencing technology to determine the full-length 16 S rRNA gene sequences from the metagenomes of 296 samples of different types of Daqu collected from ten provinces in China, and revealed the bacterial diversity at the species level in the Daqu samples. We totally identified 310 bacteria species, including 78 highly abundant species (with a relative abundance >0.1% each) which accounted for 91.90% of the reads from all the Daqu samples. We also recognized the differentially enriched bacterial species in different types of Daqu, and in the Daqu samples with the same type but from different provinces. Specifically, Lactobacillales, Enterobacterales and Bacillaceae were significantly enriched in the LTD, MTD and HTD groups, respectively. The potential co-existence and exclusion relationships among the bacteria species involved in all the Daqu samples and in the LTD, MTD and HTD samples from a specific region were also identified. These results provide a better understanding of the bacterial diversity in different types of Daqu at the species level.

Dynamic changes in volatile profiles and bacterial communities during natural fermentation of Mei yu, traditional Chinese fermented fish pieces

Microbial metabolism is important for the unique flavor formation of Mei yu, a kind of traditional Chinese fermented fish pieces. However, the interactive relationship between microorganisms and flavor components during fermentation is still unclear. In this study, electronic nose and headspace-solid-phase microextraction-gas chromatography-mass spectrometry analysis were performed to identify flavor components in Mei yu during the fermentation, and the absolute microbial quantification was conducted to identify the diversity and succession of microbial communities. During fermentation, there was an increase in the types of volatile compounds. Alcohols, aldehydes, aromatics and esters were the main flavor compounds and significantly increased in Mei yu, while hydrocarbon and aldehydes significantly decreased. The absolute abundances of Lactobacillus, Lactococcus and Weissella increased significantly after 3 days' fermentation, which were closely associated with the productions of 1-nonanol, 2-methoxy-4-vinylphenol, guaiacol, ethyl palmitate and ethyl caprylate that might though pathways related to fatty acid biosynthesis and amino acid metabolism. However, these genera were negatively correlated with the production of indole. Additionally, the total volatile basic nitrogen (TVB-N) levels of Mei yu fermented during 3 days were within the limits of 25 mg TVB-N/100 g fish, with the contents of free amino acids and lipoxygenase activities were significant lower than that of 4 days' fermentation. In view of food safety and flavor, it suggested that the natural fermented Mei yu at room temperature should be controlled within 3 days. This study highlights the application of absolute quantification to microbiome analysis in traditional fermented Mei yu and provides new insights into the roles of microorganisms in flavor formation during fermentation.

Thermal desorption-photoionization ion mobility-electronic nose (TD-PIM-Nose) with distance-probability joint decision SVM algorithm: A novel system for Daqu Grade identification

Electronic nose is a bionic technology that uses sensor arrays and pattern recognition algorithms to mimic the human olfactory system. This study developed a thermal desorption-photoionization ion mobility-electronic nose (TD-PIM-Nose) system, employing thermal desorption for direct sampling and humidity control, with a photoionization ion mobility tube as virtual sensor array for component separation and detection, and pattern recognition algorithms for signal processing to differentiate and identify samples. Furthermore, it was applied to assess four quality grades of Daqu samples ("Excellent+", "Excellent", "Grade I", and "Grade II") determined by the Check-All-That-Apply (CATA) method. Characteristic compound differences among these grades were identified using fingerprint spectra and reduced mobility values. A distance-probability joint decision support vector machine (SVM) algorithm model was established, validated against sensory CATA standards. Results showed identification accuracies: 90 %, 90 %, 96.88 %, and 100 % for respective grades. These findings demonstrated the promising potential of the TD-PIM-Nose system in Daqu quality grading.

Targeted microbial collaboration to enhance key flavor metabolites by inoculating Clostridium tyrobutyricum and Saccharomyces cerevisiae in the strong-flavor Baijiu simulated fermentation system

Ethyl hexanoate and ethyl butyrate are indispensable flavor metabolites in strong-flavor Baijiu (SFB), but batch production instability in fermenting grains can reduce the quality of distilled Baijiu. Biofortification of the fermentation process by designing a targeted microbial collaboration pattern is an effective method to stabilize the quality of Baijiu. In this study, we explored the metabolism under co-culture liquid fermentation with Clostridium tyrobutyricum DB041 and Saccharomyces cerevisiae YS219 and investigated the effects of inoculation with two functional microorganisms on physicochemical factors, flavor metabolites, and microbial communities in solid-state simulated fermentation of SFB for the first time. The headspace solid-phase microextraction-gas chromatography-mass spectrometry results showed that ethyl butyrate and ethyl hexanoate significantly increased in fermented grain. High-throughput sequencing analysis showed that Pediococcus, Lactobacillus, Weissella, Clostridium_sensu_stricto_12, and Saccharomyces emerged as the dominant microorganisms at the end of fermentation. Co-occurrence analysis showed that ethyl hexanoate and ethyl butyrate were significantly correlated (|r| > 0.5, P < 0.05) with a cluster of interactions dominated by lactic acid bacteria (Pediococcus, Lactobacillus, Weissella, and Lactococcus), which was driven by the functional C. tyrobutyricum and S. cerevisiae. Mantel test showed that moisture and reducing sugars were the main physicochemical factor affecting microbial collaboration (|r| > 0.7, P < 0.05). Taken together, the collaborative microbial pattern of inoculation with C. tyrobutyricum and S. cerevisiae showed positive results in enhancing typical flavor metabolites and the synergistic effects of microorganisms in SFB.

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.

Bioturbation analysis of microbial communities and flavor metabolism in a high-yielding cellulase Bacillus subtilis biofortified Daqu

In this study, a fortified Daqu (FF Daqu) was prepared using high cellulase-producing Bacillus subtilis, and the effects of in situ fortification on the physicochemical properties, flavor, active microbial community and metabolism of Daqu were analyzed. The saccharification power, liquefaction power, and cellulase activity of the FF Daqu were significantly increased compared with that of the traditional Daqu (CT Daqu). The overall differences in flavor components and their contents were not significant, but the higher alcohols were lower in FF Daqu. The relative abundance of dominant active species in FF Daqu was 85.08% of the total active microbiota higher than 63.42% in CT Daqu, and the biomarkers were Paecilomyces variotii and Aspergillus cristatus, respectively. The enzymes related to starch and sucrose metabolic pathways were up-regulated and expressed in FF Daqu. In the laboratory level simulation of baijiu brewing, the yield of baijiu was increased by 3.36% using FF Daqu.

The bacteriome-coupled phage communities continuously contract and shift to orchestrate the traditional rice vinegar fermentation

Amounts of microbiome studies have uncovered the microbial communities of traditional food fermentations, while in which the phageome development with time is poorly understood. Here, we conducted a study to decipher both phageome and bacteriome of the traditional rice vinegar fermentation. The vinegar phageomes showed significant differences in the alpha diversity, network density and clustering coefficient over time. Peduoviridae had the highest relative abundance. Moreover, the phageome negatively correlated to the cognate bacteriome in alpha diversity, and undergone constantly contracting and shifting across the temporal scale. Nevertheless, 257 core virial clusters (VCs) persistently occurred with time whatever the significant impacts imposed by the varied physiochemical properties. Glycoside hydrolase (GH) and glycosyltransferase (GT) families genes displayed the higher abundances across all samples. Intriguingly, diversely structuring of toxin-antitoxin systems (TAs) and CRISPR-Cas arrays were frequently harbored by phage genomes. Their divergent organization and encoding attributes underlie the multiple biological roles in modulation of network and/or contest of phage community as well as bacterial host community. This phageome-wide mapping will fuel the current insights of phage community ecology in other traditional fermented ecosystems that are challenging to decipher.

Quantitative characterization and dynamics of bacterial communities in ready-to-eat chicken using high-throughput sequencing combined with internal standard-based absolute quantification

Ready-to-eat (RTE) chicken products are prone to bacterial contamination, posing foodborne illness risks. High-throughput sequencing (HTS) has been widely used to study the distribution of pathogenic and spoilage bacteria in RTE chicken products but lacks quantitative data on taxa abundances. In this study, we employed a method combining HTS with absolute quantification, using Edwardsiella tarda as an internal standard strain, to achieve the relative and absolute abundances of microbiota in RTE chicken products stored at 4 and 25 °C. The results showed that the addition of appropriate concentration of internal standard strains exhibited no significant impact on the structure composition, relative abundance, and absolute abundance of bacterial communities in chicken meat, achieving comprehensive absolute quantification in RTE chicken products. Furthermore, the absolute abundance of bacterial genera at the end of storage followed a log-normal distribution, with most genera having an absolute abundance between 103 and 105 CFU/g. This study provides insights into the quantification of bacterial communities in RTE chicken products, laying a foundation for the development of strategies to extend the shelf life of RTE products.

Comprehensive analysis of flavor formation mechanisms in the mechanized preparation Cantonese soy sauce koji using absolute quantitative metabolomics and microbiomics approaches

Based on the widespread application and under-research of mechanized preparation Cantonese soy sauce koji (MP), absolute quantitative approaches were utilized to systematically analyze the flavor formation mechanism in MP. The results indicated that the enzyme activities increased greatly during MP fermentation, and 4 organic acids, 15 amino acids, and 2 volatiles were identified as significantly different flavor actives. The flavor parameters of MP4 were basically identical to those of MP5. Furthermore, microorganisms were dominated by Staphylococcus, Weissella, and Aspergillus in MP, and their biomass demonstrated an increasing trend. A precise enumeration of microorganisms exposed the inaccuracy of relative quantitative data. Concurrently, Staphylococcus and Aspergillus were positively correlated with numerous enzymes and flavor compounds, and targeted strains for enhancing MP quality. The flavor formation network comprises pathways including carbohydrate metabolism, lipid metabolism and oxidation, and protein degradation and amino acid metabolism. In summary, the fermentation period of MP can be substantially shortened without compromising the product quality. These findings lay the groundwork for refining parameters in modern production processes.

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.

The insights into the phage communities of fermented foods in the age of viral metagenomics

Phages play a critical role in the assembly and regulation of fermented food microbiome through lysis and lysogenic lifestyle, which in turn affects the yield and quality of fermented foods. Therefore, it is important to investigate and characterize the diversity and function of phages under complex microbial communities and nutrient substrate conditions to provide novel insights into the regulation of traditional spontaneous fermentation. Viral metagenomics has gradually garnered increasing attention in fermented food research to elucidate phage functions and characterize the interactions between phages and the microbial community. Advances in this technology have uncovered a wide range of phages associated with the production of traditional fermented foods and beverages. This paper reviews the common methods of viral metagenomics applied in fermented food research, and summarizes the ecological functions of phages in traditional fermented foods. In the future, combining viral metagenomics with culturable methods and metagenomics will broaden the scope of research on fermented food systems, revealing the complex role of phages and intricate phage-bacterium interactions.

Exploring the heterogeneity of community and function and correspondence of "species-enzymes" among three types of Daqu with different fermentation peak-temperature via high-throughput sequencing and metagenomics

The enzyme activity of Daqu is an important prerequisite for defining it as a Baijiu starter. However, little is known about the functional species related to enzymes in different types of Daqu at the metagenomic level. Therefore, we analyzed the differences in enzymatic properties, microbial composition and metabolic function of three types of Daqu, namely high-, medium- and low-temperature Daqus (HTD, MTD and LTD), by combining chemical feature and multi-dimensional sequencing. The results showed that both liquefaction, saccharification, fermentation and esterification powers were remarkably weaker in HTD compared to MTD and LTD. Totally, 30 bacterial and 5 fungal phyla were identified and significant differences in community structures were also observed among samples, with Brevibacterium/Microascus, Pseudomonas, and Lactobacillus/Saccharomycopsis identified as biomarkers for HTD, MTD and LTD, respectively. Additionally, the importance of deterministic assembly in bacterial communities was proportional to the fermentation peak-temperature, while stochastic assembly dominated in fungal ones. Metagenomics analysis indicated eukaryota (>80 %, mainly Ascomycota) predominated in HTD and MTD while bacteria (54.3 %, mainly Actinobacteriota) were more abundant in LTD. However, the functional profiles and pathways of MTD and LTD were more similar, and the synthesis and metabolism of carbohydrates and amino acids were the crucial biological functions of all samples. Finally, the relationship between species and enzymes in different samples was constructed and the functional species in LTD and MTD were more diverse than HTD, which elucidated the functional species associated with enzyme activity in each type of Daqu. These results will greatly enrich our understanding of the core functional species in three typical Daqu, which provide available information for rational regulation of Daqu quality and the Baijiu fermentation.

Bacteria and filamentous fungi running a relay race in Daqu fermentation enable macromolecular degradation and flavor substance formation

As the saccharifying and fermentative agent, medium-temperature Daqu (MT-Daqu) plays an irreplaceable role in the production of strong-flavor Baijiu. Numerous studies have focused on the microbial community structure and potential functional microorganisms, however, little is known about the succession of active microbial community and the formation mechanism of community function during MT-Daqu fermentation. In this study, we presented an integrated analysis of metagenomics, metatranscriptomics, and metabonomics covering the whole fermentation process of MT-Daqu to reveal the active microorganisms and their participations in metabolic networks. The results showed that dynamic of metabolites were time-specific, and the metabolites and co-expressed active unigenes were further classified into four clusters according to their accumulation patterns, with members within each cluster displaying a uniform and clear pattern of abundance across fermentation. Based on KEGG enrichment analysis in co-expression clusters and succession of active microbial community, we revealed that Limosilactobacillus, Staphylococcus, Pichia, Rhizopus, and Lichtheimia were metabolically active members at the early stage, and their metabolic activities were conducive to releasing abundant energy to drive multiple basal metabolisms such as carbohydrates and amino acids. Thereafter, during the high temperature period and at the end of fermentation, multiple heat-resistant filamentous fungi were transcriptionally active populations, and they acted as both the saccharifying agents and flavor compound producers, especially aromatic compounds, suggesting their crucial contribution to enzymatic activity and aroma of mature MT-Daqu. Our findings revealed the succession and metabolic functions of the active microbial community, providing a deeper understanding of their contribution to MT-Daqu ecosystem.

Exploration of seasonal fermentation differences and the possibility of flavor substances as regulatory factors in Daqu

Medium-high temperature Daqu is a characteristic starter for Chinese strong-flavor Baijiu fermentation, and its final quality determines the character and type of Baijiu. Nonetheless, its formation is affected by the interaction of physical and chemical, environmental and microbial interaction, and the differences in seasonal fermentation performance emerge. Here, the differences in the two seasons' Daqu fermentation properties were revealed by the detection of the enzyme activity. The respective dominant enzyme in summer Daqu (SUD) was protease and amylase, while cellulase and glucoamylase in spring Daqu (SPD). The underlying causes of this phenomenon were then investigated through an evaluation of nonbiological variables and microbial community structure. A greater absolute number of microorganisms, particularly Thermoactinomyces, were created in the SPD as a result of the superior growth environment (higher water activity). Additionally, the correlation network and discriminant analysis hypothesized that the volatile organic compound (VOC) guaiacol, which had a different content between SUD and SPD, may be a contributing element to the microbial composition. In contrast to SUD, the enzyme system activity related to guaiacol production in SPD was significantly higher. To support this notion that the volatile flavor chemicals mediate microbial interactions in Daqu, the growth effect of guaiacol on several bacteria isolated from the Daqu was examined in both a contact and non-contact manner. This study emphasized that VOCs not only have the basic characteristics of flavor compounds but also have ecological significance. Because the strains' varied structures and enzyme activities affected how the microorganisms interacted, the VOCs produced in this way ultimately had a synergistic effect on the various effects of Daqu fermentation.

Analysis of the Influence of Microbial Community Structure on Flavor Composition of Jiang-Flavor Liquor in Different Batches of Pre-Pit Fermented Grains

To explore the effects of microbial community changes on the key flavor substances in base Baijiu, this study analyzed the microbiome of the pre-pit fermentation grains using high-throughput sequencing technology and determined the flavor substances of the base Baijiu by GC-FID. The results showed the microbial community changed dynamically between the different rounds, as well as bacteria and fungi displayed different succession patterns. Next, the variations of skeletal flavor substances in the base Baijiu were analyzed by multiomics, and it was found that alcohols, acids, and esters were the most abundant, accounting for 88.16–98.87% of the total flavor substances, and decreased with the increase of the rounds. By calculating the Spearman coefficient, it was found that microorganisms such as Acinetobacter, Oceanobacillus, Saccharomyces, and Byssochlamys were significantly correlated with the n-Propano and 2,3-Butanediol and other components in the base Baijiu. Finally, 15 flavor substances such as Acetaldehyde, Propionaldehyde, and Isobutyraldehyde were identified as key substances by OAV analysis. This study is the first to reveal the potential association between the microbial community of pre-pit fermentation grains and flavor of base Baijiu and has the benefit of improving the quality of base Baijiu.