Characterisation and comparison of the microflora of traditional and pure culturexiaoquduring thebaijiuliquor brewing process

Core microbes identification and synthetic microbiota construction for the production of Xiaoqu light-aroma Baijiu

Baijiu production has relied on natural inoculated Qu as a starter culture, causing the unstable microbiota of fermentation grains, which resulted in inconsistent product quality across batches. Therefore, revealing the core microbes and constructing a synthetic microbiota during the fermentation process was extremely important for stabilizing product quality. In this study, the succession of the microbial community was analyzed by high-throughput sequencing technology, and ten core microbes of Xiaoqu light-aroma Baijiu were obtained by mathematical statistics, including Acetobacter, Bacillus, Lactobacillus, Weissella, Pichia,Rhizopus, Wickerhamomyces, Issatchenkia, Saccharomyces, and Kazachstania. Model verification showed that the core microbiota significantly affected the composition of non-core microbiota (P < 0.01) and key flavor-producing enzymes (R > 0.8, P < 0.01), thus significantly affecting the flavor of base Baijiu. Simulated fermentation validated that the core microbiota can reproduce the fermentation process and quality of Xiaoqu light-aroma Baijiu. The succession of bacteria was mainly regulated by acidity and ethanol, while the fungi, especially non-Saccharomyces cerevisiae, were mainly regulated by the initial dominant bacteria (Acetobacter, Bacillus, and Weissella). This study will play an important role in the transformation of Xiaoqu light-aroma Baijiu fermentation from natural fermentation to controlled fermentation and the identification of core microbes in other fermented foods.

Unveiling the microbiota of sauce-flavor Daqu and its relationships with flavors and color during maturation

This study investigated the microbial community in three-color sauce-flavor Daqu (black, yellow, and white) throughout their maturation processes, together with their physicochemical factors, culturable microbes, flavor components, and fermenting vitalities. Results from high-throughput sequencing revealed distinct microbial diversity, with more pronounced variations in bacterial community than in fungal community. Firmicutes and Ascomycota emerged as the most dominant bacterial and fungal phyla, respectively, during maturation. Genus-level analysis identified Kroppenstedia, Virgibacillus, and Bacillus as dominant bacteria in black Daqu, yellow Daqu, and white Daqu, severally, while Thermoascus was shared as the core dominant fungi for these Daqu. Physicochemical factors, particularly acidity, were found to exert a significant impact on microbial community. Kroppenstedtia was the key bacteria influencing the color formation of these Daqu. Furthermore, correlations between dominant microbes and flavor compounds highlighted their role in Daqu quality. Molds (Aspergillus, Rhizomucor, and Rhizopus), excepting Bacillus, played a crucial role in the formation of pyrazine compounds. Consequently, this study offers innovative insights into the microbial perspectives on color and pyrazine formation, establishing a groundwork for future mechanized Daqu production and quality control of sauce-flavor baijiu.

Insights into the Dynamic Succession of Microbial Community and Related Factors of Vanillin Content Change Based by High-Throughput Sequencing and Daqu Quality Drivers

Daqu is an important saccharifying starter in the fermentation of Nongxiangxing Baijiu in China. Vanillin is a health and flavor factor in Baijiu. However, only a few research studies on the vanillin content of Daqu are currently not systematic. In order to investigate the metabolic mechanism of vanillin in the fermentation process of Daqu, we analyzed the changes in microorganisms, influencing factors, and enzymes related to vanillin in Daqu. This research found that there were differences between bacterial and fungal genera in each sample, and the abundance of bacteria was greater than that of fungi. Among the microbial genera, Klebsiella, Escherichia, Acinetobacter, Saccharopolyspora, Aerococcus, and Puccinia were positively correlated with vanillin. Meanwhile, we also found that moisture and reducing sugar were the main physicochemical factors affecting the formation of vanillin. The functional annotation results indicate that carbohydrate metabolism and energy metabolism were important microbial metabolic pathways that impacted vanillin production in solid-state fermentation. The feruloyl-CoA hydratase/lyase (EC 4.1.2.61) and acylamidase (EC 3.5.1.4) were positively correlated with vanillin content (p ≤ 0.05) and promote the increase in vanillin content. These findings contribute to furthering our understanding of the functional microorganisms, physicochemical factors, and enzymes related to the change in vanillin content during the fermentation of Daqu and can help to further explore the flavor substances in Baijiu fermentation in the future.

Ultra-high-depth macrogenomic sequencing revealed differences in microbial composition and function between high temperature and medium-high temperature Daqu

Complex microorganisms in Daqu of different temperatures play a vital role in the taste, flavor and quality of Baijiu during fermentation. However, understanding the functional diversity of the whole microbial community between the Daqus of two different temperatures (high temperature Daqu, HD and medium-high temperature Daqu, MD) remains a major challenge. Here, a systematic study of the microbial diversity, functions as well as physiological and biochemical indexes of Daqu are described. The results revealed that the Daqu exhibited unique characteristics. In particular, the diversity of microorganisms in HD and MD was high, with 44 species including 14 novel species (Sphingomonas sp. is the main novel species) detected in all samples. Their profiles of carbohydrate-active enzymes and specific functional components supported the fact that these species were involved in flavor formation. The Daqu microbiome consisted of a high proportion of phage, providing evidence of phage infection/genome integration and horizontal gene transfer from phage to bacteria. Such processes would also regulate Daqu microbiomes and thus flavor quality. These results enrich current knowledge of Daqu and can be used to promote the development of Baijiu fermentation technology.

Uncovering acid resistance genes in lactic acid bacteria and impact of non-viable bacteria on bacterial community during Chinese strong-flavor baijiu fermentation

Chinese strong-flavor baijiu (CSFB) brewing is a spontaneously solid-state fermentation process for approximately 60 days. Numerous microorganisms grow, die, and spark a series of metabolic reactions during fermentation. In this study, the microbial community and structure between total and viable bacteria in zaopei from the 5- and 20-year pits of CSFB are revealed by amplicon sequencing. Metagenome sequencing was applied to investigate acid resistance genes in Lactobacillus and predict carbohydrate active enzyme in zaopei. Besides, SourceTracker was conducted to expose bacterial sources. Results revealed that there was no significant difference in the bacterial community and structure between the total and viable bacteria; Lactobacillus was the most dominant bacterium in zaopei of two types of pits. Meanwhile, acid resistance genes argR, aspA, ilvE, gshA, DnaK, and cfa were genes that sustained Lactobacillus survival in the late stages of fermentation with high contents of acid and ethanol, and glycosyltransferases were identified as the predominated enzymes during the CSFB fermentation which catalyzed the process of lactic acid generation via Embden-Meyerhof-Parnas pathway and Hexose Monophosphate Pathway. Moreover, the environment contributed most bacteria to zaopei of the 5- and 20-year pits. These findings will provide a deeper understanding of the microbial community structure of viable and total bacteria and the reason for the dominance of Lactobacillus in the later stages of CSFB fermentation.

Integrated multi-omics approaches to understand microbiome assembly in Jiuqu, a mixed-culture starter

The use of Jiuqu as a saccharifying and fermenting starter in the production of fermented foods is a very old biotechnological process that can be traced back to ancient times. Jiuqu harbors a hub of microbial communities, in which prokaryotes and eukaryotes cohabit, interact, and communicate. However, the spontaneous fermentation based on empirical processing hardly guarantees the stable assembly of the microbiome and a standardized quality of Jiuqu. This review describes the state of the art, limitations, and challenges towards the application of traditional and omics-based technology to study the Jiuqu microbiome and highlights the need for integrating meta-omics data. In addition, we review the varieties of Jiuqu and their production processes, with particular attention to factors shaping the microbiota of Jiuqu. Then, the potentials of integrated omics approaches used in Jiuqu research are examined in order to understand the assembly of the microbiome and improve the quality of the products. A variety of different approaches, including molecular and mass spectrometry-based techniques, have led to scientific advances in the analysis of the complex ecosystem of Jiuqu. To date, the extensive research on Jiuqu has mainly focused on the microbial community diversity, flavor profiles, and biochemical characteristics. An integrative approach to large-scale omics datasets and cultivated microbiota has great potential for understanding the interrelation of the Jiuqu microbiome. Further research on the Jiuqu microbiome may explain the inherent property of compositional stability and stable performance of a complex microbiota coping with environmental perturbations and provide important insights to reconstruct synthetic microbiota and develop modern intelligent manufacturing procedures for Jiuqu.

RETRACTED: Unraveling the composition and succession of microbial community and its relationship to flavor substances during Xin-flavor baijiu brewing

This article has been retracted: please see Elsevier Policy on Article Withdrawal (http://www.elsevier.com/locate/withdrawalpolicy). This article has been retracted at the request of the authors. The authors reported unauthorized use of several figures in this paper of copyrighted material from the Daohuaxiang Liquor Co., Ltd. Therefore, the authors are retracting the paper in its entirety. They apologize for any inconvenience this may have caused.

Chinese Baijiu: The Perfect Works of Microorganisms

Chinese Baijiu is one of the famous distilled liquor series with unique flavors in the world. Under the open environment, Chinese Baijiu was produced by two solid-state fermentation processes: jiuqu making and baijiu making. Chinese Baijiu can be divided into different types according to the production area, production process, starter type, and product flavor. Chinese Baijiu contains rich flavor components, such as esters and organic acids. The formation of these flavor substances is inseparable from the metabolism and interaction of different microorganisms, and thus, microorganisms play a leading role in the fermentation process of Chinese Baijiu. Bacteria, yeasts, and molds are the microorganisms involved in the brewing process of Chinese Baijiu, and they originate from various sources, such as the production environment, production workers, and jiuqu. This article reviews the typical flavor substances of different types of Chinese Baijiu, the types of microorganisms involved in the brewing process, and their functions. Methods that use microbial technology to enhance the flavor of baijiu, and for detecting flavor substances in baijiu were also introduced. This review systematically summarizes the role and application of Chinese Baijiu flavor components and microorganisms in baijiu brewing and provides data support for understanding Chinese Baijiu and further improving its quality.

Effects of ultra-long fermentation time on the microbial community and flavor components of light-flavor Xiaoqu Baijiu based on fermentation tanks

Microbial structure and succession of fermented grains play a significant role in Baijiu's flavor and quality. In this study, high-throughput sequencing (HTS) coupled with headspace solid-phase microextraction-gas chromatography-mass spectrometry (HS-SPME-GC-MS) were used to analyze the microbial community structures and flavor components in the fermented grains at the end of fermentation from different fermentation time of light-flavor Xiaoqu Baijiu. HTS results showed that Lactobacillus acetotolerans, Lactobacillus helveticus, Lactobacillus buchneri, Wickerhamomyces, Saccharomyces, and Condenascus were identified as the dominant microbes, but Lactobacillus (96.28%) exhibited obvious advantages at the end of ultra-long fermentation time (day 98). HS-SPME-GC-MS analysis revealed that esters and alcohols had the most abundance in fermented grains of day 98, containing high concentrations of ethyl acetate, diethyl succinate, phenylethyl alcohol, isoamyl alcohol, and n-propanol, which were related to the succession of Lactobacillus and yeast communities. Interestingly, the content of n-propanol in the ultra-long fermentation time samples (day 98) was 6 times of that in normal fermented grains (day 14), which may be caused by higher abundance of Lactobacillus in day 98 samples. Monte Carlo permutation test showed residual starch, acidity, and amino nitrogen (p < 0.05) were important factors affecting the microbial community. Together, these results shed light on the physicochemical changes, microbial dynamics, and key flavor components of fermented grains at the end of fermentation from different fermentation time and provide a strategy for further improvement of Baijiu quality.

Deciphering Succession and Assembly Patterns of Microbial Communities in a Two-Stage Solid-State Fermentation System

Although the importance of microbiota in the natural environment and in industrial production has been widely recognized, little is known about the formation and succession patterns of the microbial community, particularly secondary succession after disturbance. Here, we choose the Xiaoqu liquor brewing process as an experimental model in which sorghum grains were first aerobically saccharified and then anaerobically fermented after being stirred and acidified to explore multistage community succession patterns. We analyzed microbial composition, physicochemical factors, and metabolites of brewing grains inoculated with two different starters, pure starter and traditional starter, respectively. Two groups showed similar succession patterns where the saccharification microbiota was mainly derived from starters, while environmental microorganisms, mainly Lactobacillaceae and Saccharomyces, dominated the fermentation microbiota regardless of the original saccharification community composition. Species replacement shaped the bacterial community, while species replacement and loss both contributed to fungal community succession in both groups. Grain acidification and hypoxia led to the succession of bacterial and fungal communities during fermentation, respectively. Despite inoculation with starters containing different microorganisms, similar microbial communities during the fermentation stage of the two groups exhibited similar metabolite composition. However, higher abundance of Rhizopus in the saccharification of the pure starter group led to more alcohols, while higher abundance of Monascus and Saccharomycopsis in the traditional starter group promoted acid and ester metabolism. These results revealed the microbial succession patterns of two-stage liquor brewing and its influence on flavor metabolism, which could be used to regulate the microbial community in food fermentation to further promote the modernization of the fermented food industry.

IMPORTANCE Revealing formation and assembly mechanisms of microbiota can help us to understand and further regulate its roles in the ecosystems. The Xiaoqu liquor brewing system is a tractable microbial ecosystem with low complexity. This two-stage microbial ecosystem can be used as an experimental model to analyze the multistage temporal succession pattern of microbial communities. Our results demonstrated the dynamic composition and succession pattern of a microbial community in the two-stage liquor brewing system. The results also revealed the microbial origins determining community composition, the ecological processes dominating microbial community succession patterns, the determinants affecting microbial community successions, and the effect of microbial community changes on metabolite synthesis. Overall, our study not only provides an insight into multistage succession patterns of microbial communities in liquor brewing systems but also provides reference for optimizing the quality of fermented products, which will be helpful to understand the succession patterns of microbial communities in other natural ecosystems.

Detection of viable and total fungal community in zaopei of Chinese strong-flavor baijiu using PMA combined with qPCR and HTS based on ITS2 region

Background

Chinese strong-flavor baijiu (CSFB), one of the three major baijiu types, is the most popular baijiu type among consumers in China. A variety of microbes are involved in metabolizing raw materials to produce ethanol and flavor substances during fermentation, which fundamentally determined the quality of baijiu. It is of great importance to study microbial community of fermented grains (zaopei) during baijiu brewing process for improving its quality. In this study, we firstly used propidium monoazide (PMA) to treat zaopei samples from 5-year pit and 20-year pit for removing the interference of non-viable fungi, and analyzed the diversity of total fungi and viable fungi by quantitative PCR (qPCR) and high-throughput sequencing (HTS) based on ITS2 gene.

Results

The results showed that total fungi and viable fungi displayed no significant differences at OTU, phylum, or genus levels during fermentation within two kinds of pits. A total of 6 phyla, 19 classes, and 118 genera in fungi were found based on OTUs annotation in zaopei samples from 5-year pit and 20-year pit. Besides, non-viable fungi had little effect on the fungal community diversity during the fermentation cycle. It was found that the most dominant viable fungi belonged to Saccharomyces, Kazachstania, Naumovozyma, and Trichosporon, and Naumovozyma was firstly detected in zaopei samples of CSFB. Moreover, based on the variation of flavor substances in zaopei samples, the quality of CSFB produced from older pit was better than that produced from younger pit.

Conclusion

The non-viable fungi had little effect on the fungal diversity, structure, and relative abundance in zaopei samples of CSFB, and Naumovozyma was firstly detected in zaopei samples of CSFB. Our findings can be applied as guidance for improving the quality and stability of CSFB.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02334-8.

Deciphering the Shifts in Microbial Community Diversity From Material Pretreatment to Saccharification Process of Fuyu-Flavor Baijiu

The microbiota of the pretreatment phase is crucial to the assembly of the microbial community in the saccharification of fuyu-flavor baijiu. This study investigates the shifts in microbial community diversity from the pretreatment of raw materials to the end of saccharification. High-throughput sequencing reveals that Lactobacillus, Weissella, and Bacillus in the bacterial community and Rhizopus, Candida, Pichia, and Aspergillus in the fungal community are predominant during raw material pretreatment and saccharification processes. Also, 11 bacterial genera, including Bacillus, Lactobacillus, Leuconostoc, Weissella, Lactococcus, and Acetobacter, and eight yeast genera, including Candida, Pichia, Saccharomyces, and Wickerhamomyces, were isolated from the initial saccharification stage by culture-dependent approaches. Sourcetracker analysis indicates that the cooling grains and rice husks were the main contributors to the bacterial community composition of the saccharification process, and Qu was the main contributor to the shaping of the fungal community structure during the saccharification process. Abundance variation of the predictive functional profiles of microbial communities encoding for key enzymes involved in pyruvate metabolism, starch and sucrose metabolism, and glycolysis/gluconeogenesis during the pretreatment and saccharification phases were inferred by PICRUSt2 analysis. The results of this study will be utilized to produce consistently high-quality fuyu-flavor baijiu via better controlling the shaping of microbial community structures during the pretreatment and fermentation processes.

Characteristics of the Microbial Community in the Production of Chinese Rice-Flavor Baijiu and Comparisons With the Microflora of Other Flavors of Baijiu

Rice-flavor baijiu is one of the four basic flavor types of Chinese baijiu. Microbial composition plays a key role in the classification of baijiu flavor types and the formation of flavor substances. In this study, we used high-throughput sequencing technology to study the changes of microbial community in the production of rice-flavor baijiu, and compared the microbial community characteristics during production of rice-, light-, and strong-flavor baijiu. The results showed that the species diversity of bacteria was much higher than that of fungi during the brewing of rice-flavor baijiu. The bacterial diversity index first increased and then decreased, while the diversity of fungi showed an increasing trend. A variety of major microorganisms came from the environment and raw rice materials; the core bacteria were Lactobacillus, Weissella, Pediococcus, Lactococcus, Acetobacter, etc., among which Lactobacillus was dominant (62.88-99.23%). The core fungi were Saccharomyces (7.06-83.50%) and Rhizopus (15.21-90.89%). Temperature and total acid content were the main physicochemical factors affecting the microbial composition. Non-metric multidimensional scaling analysis showed that during the fermentation of rice-, light-, and strong-flavor baijiu, their microbial communities formed their own distinct systems, with considerable differences among different flavor types. Compared with the other two flavor types of baijiu, in the brewing process of rice-flavor baijiu, microbial species were fewer and dominant microorganisms were prominent, which may be the main reason for the small variety of flavor substances in rice-flavor baijiu. This study provides a theoretical basis for the production of rice-flavor baijiu, and lays a foundation for studying the link between baijiu flavor formation and microorganisms.

Integrative Metagenomics-Metabolomics for Analyzing the Relationship Between Microorganisms and Non-volatile Profiles of Traditional Xiaoqu

Xiaoqu, one of three traditional jiuqu in China, is a saccharifying and fermenting agent used in Xiaoqu jiu brewing, with different ingredient compositions and preparation techniques used in various regions. The yield and quality of Xiaoqu jiu are significantly affected by the metabolites and microbiota of Xiaoqu; however, the associated relationship remains poorly understood. This study aimed to analyze this relationship in three typical traditional Xiaoqu from the Guizhou province in China. The non-volatile metabolites of Xiaoqu were detected using gas chromatography time-of-flight mass spectrometry, whereas the classification and metabolic potential of the microbiota were investigated using metagenomic sequencing. Results show that Firmicutes, Proteobacteria, and Actinobacteria represent the dominant bacterial phyla, with Lactobacillus, Bacillus, Acinetobacter, Leuconostoc, and Weissella found to be the dominant bacterial genera. Meanwhile, Ascomycota, Mucoromycota, and Basidiomycota are the dominant fungal phyla with Aspergillus, Saccharomyces, Pichia, Rhizopus, and Phycomyces being the predominant fungal genera. Functional annotation of the microbiota revealed a major association with metabolism of carbohydrates, cofactors, and vitamins, as well as amino acids. A total of 39 significantly different metabolites (SDMs) were identified that are involved in 47 metabolic pathways, primarily that of starch and sucrose; glycine, serine, and threonine; glyoxylate and dicarboxylate; pyruvate; as well as biosynthesis of pantothenate and CoA. Further, based on Spearman's correlation analysis, Aspergillus, Saccharomyces, Lactobacillus, Acetobacter, Weissella, Pantoea, Desmospora, and Bacillus are closely correlated with production of physicochemical indexes and SDMs. Moreover, the metabolic network generated for the breakdown of substrates and formation of SDMs in Xiaoqu was found to primarily center on the metabolism of carbohydrates and the tricarboxylic acid cycle. These results provide insights into the functional microorganisms and metabolic patterns present in traditional Guizhou Xiaoqu and might guide researchers in the production of stable and efficient Xiaoqu in the future.