Identification of core microbiota in the fermented grains of a Chinese strong-flavor liquor from Sichuan

Starting with screening strains to construct synthetic microbial communities (SynComs) for traditional food fermentation

With the elucidation of community structures and assembly mechanisms in various fermented foods, core communities that significantly influence or guide fermentation have been pinpointed and used for exogenous restructuring into synthetic microbial communities (SynComs). These SynComs simulate ecological systems or function as adjuncts or substitutes in starters, and their efficacy has been widely verified. However, screening and assembly are still the main limiting factors for implementing theoretic SynComs, as desired strains cannot be effectively obtained and integrated. To expand strain screening methods suitable for SynComs in food fermentation, this review summarizes the recent research trends in using SynComs to study community evolution or interaction and improve the quality of food fermentation, as well as the specific process of constructing synthetic communities. The potential for novel screening modalities based on genes, enzymes and metabolites in food microbial screening is discussed, along with the emphasis on strategies to optimize assembly for facilitating the development of synthetic communities.

Comprehensive analysis of spatial heterogeneity reveals the important role of the upper-layer fermented grains in the fermentation and flavor formation of Qingxiangxing baijiu

Different spatial positions lead to inconsistent fermentation effects and flavors, however, the spatial heterogeneity of Qingxiangxing (QXX) Baijiu remains unknown. We investigated the microbes, flavors, and physicochemical properties of different layers in fermented grains of QXX Baijiu using Illumina HiSeq sequencing, two-dimensional gas chromatography-mass spectrometry (GC × GC-MS) and ultra-high performance liquid chromatography-mass (UHPLC-MS). A total of 79 volatiles, 1596 metabolites, 50 bacterial genera, and 52 fungal genera were identified. The contents distribution followed the order: upper layer > bottom layer > middle layer. Organic acids and derivatives were the main differential metabolites across the three layers. Starch, pH, and reducing sugar levels increased from the upper to bottom layer. Saccharomyces and Lactobacillus were dominant microbes. Pediococcus, the biomarker of upper layer, showed positive correlations with formic acid, ethyl lactate, acetic acid, ethyl linoleate, and ethyl oleate. These findings deepen our understanding of the fermentation and flavor formation mechanisms of QXX Baijiu.

Characterizing the Contribution of Functional Microbiota Cultures in Pit Mud to the Metabolite Profiles of Fermented Grains

Elevating the flavor profile of strong flavors Baijiu has always been a focal point in the industry, and pit mud (PM) serves as a crucial flavor contributor in the fermentation process of the fermented grains (FG). This study investigated the influence of wheat flour and bran (MC and FC) as PM culture enrichment media on the microbiota and metabolites of FG, aiming to inform strategies for improving strong-flavor Baijiu flavor. Results showed that adding PM cultures to FG significantly altered its properties: FC enhanced starch degradation to 51.46% and elevated reducing sugar content to 1.60%, while MC increased acidity to 2.11 mmol/10 g. PM cultures also elevated FG's ester content, with increases of 0.36 times for MC-FG60d and 1.48 times for FC-FG60d compared to controls, and ethyl hexanoate rising by 0.91 times and 1.39 times, respectively. Microbial analysis revealed that Lactobacillus constituted over 95% of the Abundant bacteria community, with Kroppenstedtia or Bacillus being predominant among Rare bacteria. Abundant fungi included Rasamsonia, Pichia, and Thermomyces, while Rare fungi consisted of Rhizopus and Malassezia. Metagenomic analysis revealed bacterial dominance, primarily consisting of Lactobacillus and Acetilactobacillus (98.80-99.40%), with metabolic function predictions highlighting genes related to metabolism, especially in MC-FG60d. Predictions from PICRUSt2 suggested control over starch, cellulose degradation, and the TCA cycle by fungal subgroups, while Abundant fungi and bacteria regulated ethanol and lactic acid production. This study highlights the importance of PM cultures in the fermentation process of FG, which is significant for brewing high-quality, strong-flavor Baijiu.

Exploring the regulated effects of solid-state fortified Jiuqu and liquid-state fortified agent on Chinese Baijiu brewing

Zaopei is the direct source of Chinese liquor (Baijiu). Adding functional strains to Zaopei is a potential strategy to regulate Baijiu brewing, mainly including the two ways of solid-state fortified Jiuqu (SFJ) and liquid-state fortified agent (LFA). Here, to explore their regulated details, the response patterns of Zaopei microecosystem and the changes in the product features were comprehensively investigated. The results showed that SFJ more positively changed the physicochemical properties of Zaopei and improved its ester content, from 978.57 mg/kg to 1078.63 mg/kg over the fermentation of 30 days, while LFA decreased the content of esters, alcohols, and acids. Microbial analysis revealed that SFJ significantly increased Saccharomycopsis and Aspergillus from the start of fermentation and induced a positive interaction cluster driven by the added functional Paenibacillus, while LFA exhibited a community structure near that of the original microecosystem and led to a simpler network with the reduced microbial nodes and correlations. Metabolism analysis found that both SFJ and LFA weakened the flavor-producing metabolism by suppressing some key enzyme pathways, such as EC 3.2.1.51, EC 4.2.1.47, EC 1.1.1.27, EC 1.1.1.22, EC 1.5.1.10, EC 1.14.11.12. As a result, SFJ improved the raw liquor yield by 28.5 % and endowed the final product with a more fragrant aroma, mainly through ethyl (E)-cinnamate, ethyl isovalerate, ethyl phenacetate with the higher odor activity values, while LFA promoted the yield by 13.2 % and resulted in a purer and less intense aroma through the aroma-active β-damascenone, ethyl heptoate, ethyl phenacetate. These results facilitated the regulated mechanism of SFJ and LFA on Baijiu brewing and indicated that the used functional strains in this study could be applicated in SFJ way for the further industrial-scale application.

Exploring core functional fungi driving the metabolic conversion in the industrial pile fermentation of Qingzhuan tea

The distinct sensory quality of Qingzhuan tea is mainly formed in pile fermentation by a group of functional microorganisms but the core functional ones was poorly characterized. Therefore, this study investigated the dynamic changes in the fungal community and metabolic profile by integrating microbiomics and metabolomics, and explored the core functional fungi driving the metabolic conversion in the industrial pile fermentation of Qingzhuan tea. Indicated by microbiomics analysis, Aspergillus dominated the entire pile-fermentation process, while Thermoascus, Rasamsonia, and Cylindrium successively abounded in the different stages of the pile fermentation. A total of 50 differentially changed metabolites were identified, with the hydrolysis of galloyl/polymeric catechins, biosynthesis of theabrownins, oxidation of catechins, N-ethyl-2-pyrrolidinone substitution of catechins, and deglycosylation of flavonoid glucosides. Nine fungal genera were identified as core functional fungi, in which Aspergillus linked to the hydrolysis of polymeric catechins and insoluble polysaccharides as well as biosynthesis of theabrownins, while Thermoascus participated in the biosynthesis of theabrownins, deglycosylation of flavonoid glucosides, and N-ethyl-2-pyrrolidinone substitution of catechins. These findings would advance our understanding of the quality formation of Qingzhuan tea and provide a benchmark for precise inoculation for its quality improvement.

Daqu and environmental microbiota regulate fatty acid biosynthesis via driving the core microbiota in soy sauce aroma type liquor fermentation

Fatty acids are considered as important compounds for the aroma and taste of Chinese liquor. Revealing the core microbiota related with fatty acid biosynthesis and how they are influenced are essential to control fatty acids in spontaneous Chinese liquor fermentation. Herein, we identified the core microbiota related with fatty acid biosynthesis based on their microbial abundance, abundance and expression level of genes related with fatty acid biosynthesis, using high-throughput amplicon sequencing, metagenomic and metatranscriptomic analysis, respectively. Acetilactobacillus, Kroppenstedtia, Saccharomyces, Paecilomyces and Pichia were identified as the core microbiota (the criteria for identifying core microbiota: average relative abundance ≥1 %, average abundance of related genes >400 fragments per kilobase of transcript per million fragments mapped [FPKM], and expression level of related genes >1000 FPKM) related with fatty acid biosynthesis. SourceTracker analysis showed that Daqu mainly provided Kroppenstedtia (34.01 %) and Acetilactobacillus (3.31 %). Ground mainly provided Pichia (47.47 %), Saccharomyces (16.17 %) and Paecilomyces (8.55 %). Structural equation model revealed that Daqu and environmental microbiota drove the core microbiota (P < 0.05), and the core microbiota drove the biosynthesis of fatty acids (P < 0.05). This work revealed the important role of Daqu and environmental microbiota in fatty acid biosynthesis in liquor fermentation. It would benefit controlling fatty acids in liquor fermentation, and improving the liquor quality.

Analysis of Bacterial Diversity in Fermented Grains of Baijiu Based on Culturomics and Amplicon Sequencing

Baijiu is a traditional distilled liquor in China. The unique flavor developed during the fermentation process of Baijiu is closely related to the microorganisms in the fermented grains of the Baijiu. Fermented grain is a solid material that has not been distilled after the fermentation of Baijiu. It is of great significance to study the bacterial diversity in fermented grains and to isolate and culture them to reveal the formation mechanism of the flavor substances in Baijiu. In this study, the diversity of bacteria in fermented grains was studied by the combination of amplicon sequencing and culturomics, and a pure culture of culturable strains was obtained. The results of amplicon sequencing showed that the bacteria detected in the fermented grains were classified into 5 phyla, 8 classes, 24 orders, 34 families, and 45 genera, of which Lactobacillus (66.95%) and Acetobacter (32.36%) were the dominant genera. By using the method of culturomics, five pH gradients (pH = 3, 4, 5, 6, and 7) of enrichment culture medium and solid medium with different components were designed to enrich and isolate the culturable bacteria in the fermented grains. A total of 323 strains of bacteria were obtained, belonging to 53 genera and 118 species, and 14 suspected new species were obtained. Among the bacteria isolated by the culturomics, 14 genera were detected by amplicon sequencing, and 39 genera were not detected, indicating that the culturomics method can isolate and culture bacteria with low abundance in fermented grains. Compared with the traditional culture method, culturomics expanded the culturable bacteria in the fermented grains to 188%. The diversity of the bacteria in the fermented grains of Baijiu was analyzed by amplicon sequencing and culturomics, and the microbial community composition and relative abundance of fermented grains were comprehensively revealed. At the same time, the acquisition of more pure cultures of culturable bacteria provides more choices for the liquor-making microbial resource library.

The dynamics of microbial community and flavor metabolites during the acetic acid fermentation of Hongqu aromatic vinegar

In this study, we investigated the dynamics of microbial community and flavor metabolites during the traditional fermentation of Hongqu aromatic vinegar (HAV) and subsequently explored the potential relationship between microbiota and flavor metabolites. The microbiome analysis based on high-throughput sequencing (HTS) of amplicons demonstrated that Lactobacillus, Acetobacter and Clostridium were the dominant bacterial genera, while Alternaria, Candida, Aspergillus and Issatchenkia were the dominant fungal genera during the acetic acid fermentation (AAF) of HAV. A total of 101 volatile flavor compounds were identified through gas chromatography-mass spectrometry (GC-MS) during HAV fermentation, including esters (35), alcohols (17), aldehydes (11), acids (11), ketones (7), phenols (10), and others (10). Redundancy analysis (RDA) was used to reveal the correlation between microbiota and volatile flavor compounds. Lactobacillus and Acetobacter were the two bacterial genera that have the great influence on the production of volatile flavor components in HAV. Among them, Lactobacillus was positively correlated with a variety of ethyl esters, while Acetobacter positively contributed to the formation of several organic acids. Furthermore, the non-volatile metabolites were detected by ultra-high-performance liquid chromatography with quadrupole time-of-flight mass spectrometry (UPLC-QTOF/MS). A total of 41 dipeptides were identified during HAV fermentation, and most of them may have sensory characteristics and biological activities. RDA showed that Aspergillus, Epicoccum, Issatchenkia, Candida and Malassezia were the most influential fungal genera on non-volatile metabolites. In particular, Epicoccum was first reported in Hongqu vinegar and showed a positive correlation with the production of various organic acids. In conclusion, this study provides a scientific basis for understanding the flavor generation mechanism of HAV, and may be valuable for developing effective techniques to select suitable strains to improve the flavor quality of HAV.

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Microbial community in Hongqu aromatic vinegar was investigated by high-throughput sequencing.

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The key flavor metabolites during the acetic acid fermentation of HAV were selected through PLS-DA.

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Lactobacillus, Acetobacter and Clostridium were the predominant bacterial genera in HAV fermentation.

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Alternaria, Candida, Aspergillus and Issatchenkia were the predominant fungal genera in HAV fermentation.

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Redundancy analysis (RDA) revealed the correlation between microbiota and flavor metabolites.

Dynamic changes of bacteria communities in Moutai-flavor Daqu during storage analyzed by next generation sequencing

The quality of Moutai-flavor Baijiu is highly dependent on Moutai-flavor Daqu (MTDQ), which needs to be stored for six months before using. It brings abundant bacterium, which can metabolize various enzymes and favor compounds. But the reasonable storage time of MTDQ prepared in different seasons is still uncertain. To this end, the study revealed a detailed bacterial profile of storage MTDQ prepared in three different seasons (specifically, they were stored start from spring, summer and autumn) by using high-throughput sequencing approach (next generation sequencing). Results showed that major phyla of storage MTDQ were Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes, and Fusobacteria. The advantages of Firmicutes were Thermoactinomyces and Bacillaceae. Significant differences in bacterial community structures of MTDQ from different seasons and storage time were observed. Compared with summer and autumn MTDQ, the decrease of Thermoactinomyces and increase of Desmospora in spring MTDQ were the main differences and bacterial community structures of summer and autumn MTDQ were more similar. The variation trends of the bacteria community indicated the effective time of storage period were appropriately six months for spring MTDQ, two months for summer MTDQ and more than six months for autumn MTDQ. These results showed that the length of storage time was associated with the season, it's reasonable to adjust the storage time of MTDQ with the season.

Effect of microbial interaction on flavor quality in Chinese baijiu fermentation

Chinese baijiu brewing is an open, complex, and synergetic functional microbiota fermentation process. Microbial interaction is pivotal for the regulation of microbial structure and function in the brewing microecosystem, consequently affecting the flavor and quality of baijiu. This article mainly summarizes the effect of microbial interactions among functional microbiota on the growth performance, flavor formation, and safe quality of baijiu fermentation process. In addition, the review specifically emphasizes on the microbial interactions for the regulation of “Ethyl Caproate-Increasing and Ethyl Lactate-Decreasing” in Chinese strong-flavor baijiu. Furthermore, the construction of synthetic microbiota by metabolic characteristics of the functional microbes and their interactions for regulating and controlling flavor quality of Chinese baijiu is also reviewed and prospected.

The Mutual Influence of Predominant Microbes in Sourdough Fermentation: Focusing on Flavor Formation and Gene Transcription

The interplay between microorganisms generally plays a vital role in food fermentation. In this study, the mutual influence of Saccharomyces cerevisiae and Fructilactobacillus sanfranciscensis, the two predominant microbes in the sourdough ecosystem, were investigated in situ during fermentation. Doughs fermented with S. cerevisiae, F. sanfranciscensis, or their combination were compared regarding acid production, microbial density, and volatiles. Furthermore, in situ gene expressions were investigated using RNA-sequencing. The results showed that the presence of S. cerevisiae had no visible influence on F. sanfranciscensis, whereas F. sanfranciscensis facilitated the growth of S. cerevisiae but affected its volatile production since metabolites such as 3-methyl-1-butanol decreased. The RNA-sequencing demonstrated that S. cerevisiae significantly changed the gene transcripts implicated in amino acid metabolism in F. sanfranciscensis and may stimulate its growth suggested by the enrichment of the KEGG pathway of peptidoglycan biosynthesis.