Modelling and predicting population of core fungi through processing parameters in spontaneous starter (Daqu) fermentation

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.

Analysis on driving factors of microbial community succession in Jiuyao of Shaoxing Huangjiu (Chinese yellow rice wine)

The microbial ecosystem of fermented food is greatly disturbed by human activities.Jiuyao is important saccharification starter for brewing huangjiu. The interaction between environmental factors and microorganisms significantly affected the microbial community structure at different stages of Jiuyao manufacturing. This study combined environmental factor analysis and high-throughput sequencing technology to comprehensively analyze the specific changes of microbial community and environmental factors in each fermentation stage of Jiuyao production and their correlation. The results showed that the activities of liquefaction enzyme, glycosylation enzyme and acid protease reached the highest value on the 8 th day (192 h) after the beginning of fermentation, and the cellulase activity reached the highest value at the end of fermentation. Pediococcus（37.5 %-58.2 %）, Weissella（9.2 %-27.0 %） and Pelomonas（0.1 %-12.1 %） were the main microbial genera in the genus bacteria, and Saccharomycopsis（37.1 %-52.0 %）, Rhizopus（12.5 %-31.0 %） and Saccharomyces（4.0 %-20.5 %） were the main microbial genera in the genus fungi. The results of correlation analysis showed that the microbial communities in Jiuyao were closely related to environmental factors. Most microbial communities were positively correlated with temperature, but negatively correlated with ambient humidity, CO2 concentration, acidity and water content of Jiuyao. In addition, the transcription levels of enzymes related to microbial glucose metabolism in Jiuyao were higher in the late stage of Jiuyao fermentation. Interestingly, these enzymes had high transcription levels in fungi such as Saccharomycopsis, Rhizopus and Saccharomyces, as well as in bacteria such as Pediococcus and Lactobacillus. This study provides a reference for revealing the succession rule of microbial community structure caused by environmental factors during the preparation of Jiuyao in Shaoxing Huangjiu.

Contrasting the microbial community and non-volatile metabolites involved in ester synthesis between Qing-flavor Daqu and Nong-flavor Daqu

Daqu, a fermentation starter, was important source of key flavors of Chinese Baijiu. The quality of Chinese Baijiu could be significantly affected by the ester-synthesis microorganisms. In order to clarify the microbial community that promoted the ester formation in Daqu, the dynamic changes of microbial community and non-volatile profiles of Qing-flavor Daqu and Nong-flavor Daqu samples through the whole making process were investigated by Illumina MiSeq platform and liquid chromatograph-mass spectrometry (LC-MS). The non-volatile compounds related to ester synthesis were identified by comparing with ester synthesis pathway and partial least squares discriminant analysis (PLS-DA). Correlations between microbial community and non-volatile metabolites involved in ester synthesis of two types of Daqu were disclosed by Pearson correlation analysis. Results showed that a total of 50 key compounds involved in ester synthesis were identified and 25 primary functional microorganisms were screened in 39 samples. Among them, in Qing-flavor Daqu, the top three primary functional microorganisms that had strong correlations with ester-formation precursors were Lactobacillus, Pantoea, and Sphingomonas; Lactobacillus and Pantoea had significantly positive interactions with various microorganisms, but Sphingomonas did not interact with others. In Nong-flavor Daqu, the top three primary functional microorganisms that had strong correlations with ester-formation precursors were Candida, Apiotrichum, and Cutaneotrichosporon. Candida showed strong positive correlation with other microorganisms, whereas Apiotrichum and Cutaneotrichosporon had no interaction with other microorganisms. The study could help our understanding of the microbial metabolism process in Daqu and provided a scientific basis for a controllable and feasible fermentation system.

Synergistic effect of biotic and abiotic factors drives microbiota succession and assembly in medium-temperature Daqu

BACKGROUND

The feasibility of fortification techniques to improve the quality of medium-temperature Daqu (MTD) by inoculation functional isolates has been demonstrated. However, it is unclear what is the effect of inoculation on the controllability during the MTD fermentation process. Here, inoculated a single strain of Bacillus licheniformis, and the microbiota composed of Bacillus velezensis and Bacillus subtilis, were used to investigate the synergistic effect of biotic and abiotic factors on the succession and assembly of the MTD microbiota during the process.

RESULTS

The biotic factors promoted the proliferation of microorganisms that arrived early at the MTD. Subsequently, this alteration might inhibit microorganisms that colonized later in the MTD microecosystem, thereby assembling a different but more stable microbial community. Moreover, the biotic factors making bacterial community assembly were dominated by variable selection earlier, whereas the fungal community assembly was dominated mainly by extreme abiotic factors rather than biotic factors. Interestingly, fermentation temperature and moisture were significantly associated with the succession and assembly of the fortified MTD community. Meanwhile, the effect of the environmental variables on endogenous variables was also significant. Thus, changes in endogenous variables could be mitigated by adjusting environmental variables to regulate the process of MTD fermentation.

CONCLUSION

Biotic factors cause rapid changes of the microbiota during the MTD fermentation process, which could be controlled indirectly by regulating environmental variables. Meanwhile, a more stable MTD ecological network might be beneficial for enhancing the stability of MTD quality. © 2023 Society of Chemical Industry.

Unraveling multifunction of low-temperature Daqu in simultaneous saccharification and fermentation of Chinese light aroma type liquor

Chinese liquor is produced by a representative simultaneous saccharification and fermentation process. Daqu, as a starter of Chinese liquor fermentation, affects both saccharification and fermentation. However, it is still unclear how Daqu contributed to the simultaneous saccharification and fermentation process. Here, using Chinese light aroma type liquor as a case, we identified low-temperature Daqu-originated enzymes and microorganisms that contributed to the simultaneous saccharification and fermentation using metaproteomic analysis combined with amplicon sequencing analysis. α-Amylase and glucoamylase accounted for 95 % of total saccharifying enzymes and were identified as key saccharifying enzymes. Lichtheimia was the key producer of these two enzymes (> 90 %) in low-temperature Daqu. Daqu contributed 90 % α-amylase and 99 % glucoamylase to the initial liquor fermentation. These two enzymes decreased by 35 % and 49 % until day 15 in liquor fermentation. In addition, Daqu contributed key microbial genera (91 % Saccharomyces, 6.5 % Companilactobacillus) and key enzymes (37 % alcohol dehydrogenase, 40 % lactic acid dehydrogenase, 56 % aldehyde dehydrogenase) related with formations of ethanol, lactic acid and flavour compounds to the initial liquor fermentation. The average relative abundances of these fermentation-related key microorganisms and enzymes increased by 2.78 times and 1.29 times till day 15 in liquor fermentation, respectively. It indicated that Daqu provided saccharifying enzymes for starch hydrolysis, and provided both enzymes and microorganisms associated with formations of ethanol, lactic acid and flavour compounds for liquor fermentation. This work illustrated the multifunction of low-temperature Daqu in the simultaneous saccharification and fermentation of Chinese light aroma type liquor. It would facilitate improving liquor fermentation by producing high-quality Daqu.

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.

Functional microorganisms in Baijiu Daqu: Research progress and fortification strategy for application

Daqu is a saccharifying and fermenting starter in the production of Chinese Baijiu; its quality directly affects the quality of Baijiu. The production of Daqu is highly environment-dependent, and after long-term natural domestication, it is rich in a wide variety of microorganisms with a stable composition, which provide complex and diverse enzymes and flavor (precursor) substances and microbiota for Jiupei (Fermented grains) fermentation. However, inoculation with a relatively stable microbial community can lead to a certain upper limit or deficiencies of the physicochemical properties (e.g., saccharification capacity, esterification capacity) of the Daqu and affect the functional expression and aroma formation of the Daqu. Targeted improvement of this problem can be proposed by selecting functional microorganisms to fortify the production of Daqu. This review introduced the isolation, screening, identification and functional characteristics of culture-dependent functional microorganisms in Baijiu-brewing, the core functional microbiota community of Daqu, and the related research progress of functional microorganisms fortified Daqu, and summarized the fortifying strategies of functional microorganisms, aiming to further deepen the application of functional microorganisms fortification in Daqu fermentation and provide ideas for the flavor regulation and quality control of Baijiu.

Challenges and perspectives of quantitative microbiome profiling in food fermentations

Spontaneously fermented foods are consumed and appreciated for thousands of years although they are usually produced with fluctuated productivity and quality, potentially threatening both food safety and food security. To guarantee consistent fermentation productivity and quality, it is essential to control the complex microbiota, the most crucial factor in food fermentations. The prerequisite for the control is to comprehensively understand the structure and function of the microbiota. How to quantify the actual microbiota is of paramount importance. Among various microbial quantitative methods evolved, quantitative microbiome profiling, namely to quantify all microbial taxa by absolute abundance, is the best method to understand the complex microbiota, although it is still at its pioneering stage for food fermentations. Here, we provide an overview of microbial quantitative methods, including the development from conventional methods to the advanced quantitative microbiome profiling, and the application examples of these methods. Moreover, we address potential challenges and perspectives of quantitative microbiome profiling methods, as well as future research needs for the ultimate goal of rational and optimal control of microbiota in spontaneous food fermentations. Our review can serve as reference for the traditional food fermentation sector for stable fermentation productivity, quality and safety.

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.

A High-Throughput Absolute Abundance Quantification Method for the Characterisation of Daqu Core Fungal Communities

An inherent issue in high-throughput sequencing applications is that they provide compositional data for relative abundance. This often obscures the true biomass and potential functions of fungi in the community. Therefore, we presented a high-throughput absolute quantification (HAQ) method to quantitatively estimate the fungal abundance in Daqu. In this study, five internal standard plasmids (ISPs) were designed for the fungal ITS2 subregion with high length variations. Five ISPs were then utilised to establish standard curves with a quantitative concentration range of 103–107 cells/g, and this was used to quantify the core fungi, including Basidiomycota, Ascomycota, and Mucoromycota. Using three types of mature Daqu from different regions, we demonstrated that the HAQ method yielded community profiles substantially different from those derived using relative abundances. Then, the HAQ method was applied to the Daqu during fermentation. The initial formation of the Daqu surface occurred in the fourth stage, which was mainly driven by moisture. The key fungi that caused the initial formation of the Daqu surface included Hyphopichia burtonii, Saccharomycopsis fibuligera, and Pichia kudriavzevii. The initial formation of the Daqu core occurred in the fifth stage, which was mainly affected by moisture and reducing the sugar content. The key fungi that cause the initial formation of the Daqu core included S. fibuligera and Paecilomyces verrucosus. We conclude that the HAQ method, when applied to ITS2 gene fungal community profiling, is quantitative and that its use will greatly improve our understanding of the fungal ecosystem in Daqu.

Analysis of Bacterial Diversity in Different Types of Daqu and Fermented Grains From Danquan Distillery

Bacterial communities in high-temperature Daqu and fermented grains are important for brewing Jiang-flavor Baijiu such as Danquan Baijiu. Daqu is a saccharifying and fermenting agent, which has a significant impact on the flavor of Baijiu. However, bacterial communities in three different types of samples from the Danquan distillery (dqjq_ck, dqjqcp, and dqjp3) were still unclear, which limited further development of Danquan Baijiu. “dqjq_ck” and “dqjqcp” indicate high-temperature Daqu at days 45 and 135, respectively. “dqjp3” indicates fermented grains. In this study, the bacterial communities of three samples were analyzed by Illumina Miseq high-throughput sequencing. The bacterial communities of three samples primarily composed of thermophilic bacteria and bacteria with stress resistance. The most abundant species in dqjq_ck, dqjqcp, and dqjp3 were Comamonas, Bacillus, and unclassified Lactobacillales, respectively. The main bacteria included Bacillus, Comamonas, Myroides, Paenibacillus, Acetobacter, Kroppenstedtia, Staphylococcus, Saccharopolyspora, Planifilum, Lactobacillus, Acinetobacter, Oceanobacillus, Enterococcus, Thermoactinomyces, Lactococcus, Streptomyces, Saccharomonospora, Tepidimicrobium, Anaerosalibacter, unclassified_Lactobacillales, unclassified_Thermoactinomycetaceae_1, unclassified_Bacillaceae_2, unclassified_Bacillales, unclassified_Microbacteriaceae, unclassified_Rhodobacteraceae, unclassified_Actinopolysporineae, and unclassified_Flavobacteriaceae in three samples (percentage was more than 1% in one of three samples). In our study, the succession of microbiota in three samples representing three important stages of Danquan Baijiu brewing was revealed. This article lays a good foundation for understanding the fermentation mechanism and screening some excellent indigenous bacteria to improve the quality of Danquan Baijiu in future.

Whole-Genome Sequencing of a Potential Ester-Synthesizing Bacterium Isolated from Fermented Golden Pomfret and Identification of Its Lipase Encoding Genes

Microbial ester synthases are regarded as valuable catalysts in the food industry. Here, one strain of Acinetobacter venetianus with ester synthase-production capacity, SCSMX-3, was isolated from traditional fermented golden pomfret. It exhibited good growth in mesophilic, low salt, and slightly alkaline environments. The ester synthase produced by SCSMX-3 displayed maximum activity at pH 8.0 and 35 °C. Genome sequencing revealed that the strain contains one circular chromosome of 336313 bp and two circular plasmids (plasmid A-14424 bp and plasmid B-11249 bp). Six CRISPR structures enhance the genomic stability of SCSMX-3 and provide the opportunity to create new functional strains. Gene function analysis indicated that SCSMX-3 produces the necessary enzymes for survival under different conditions and for flavor substance synthesis. Furthermore, 49 genes encoding enzymes associated with lipid metabolism, including three triacylglycerol lipases and two esterases, were identified through the NCBI Non-Redundant Protein Database. The lipase encoded by gene0302 belongs to the GX group and the abH15.02 (Burkholderia cepacia lipase) homolog of the abH15 superfamily. Our results shed light on the genomic diversity of and lipid metabolism in A. venetianus isolated from fermented golden pomfret, laying a foundation for the exploration of new ester synthases to improve the flavor of fermented fish products.

Constructing Micro-Landscapes: Management and Selection Practices on Microbial Communities in a Traditional Fermented Beverage

Colonche is a traditional beverage produced in Mexico by the fermentation of fruits of several cacti species. In the Meridional Central Plateau region of Mexico, where this study was conducted, it is mainly produced with fruits of Opuntia streptacantha; there, the producers perform spontaneous fermentation and/or fermentations through inoculums. Several factors can change the microbial community structure and dynamics through the fermentation process, but little attention has been directed to evaluate what type and extent of change the human practices have over the microbial communities. This study aims to assess the microbiota under spontaneous and inoculated fermentation techniques, the microorganisms present in the inoculums and containers, and the changes of microbiota during the process of producing colonche with different techniques. We used next-generation sequencing of the V3-V4 regions of the 16S rRNA gene and the ITS2, to characterize bacterial and fungal diversity associated with the different fermentation techniques. We identified 701 bacterial and 203 fungal amplicon sequence variants (ASVs) belonging to 173 bacterial and 187 fungal genera. The alpha and beta diversity analysis confirmed that both types of fermentation practices displayed differences in richness, diversity, and community structure. Richness of bacteria in spontaneous fermentation (0D = 136 ± 0.433) was higher than in the inoculated samples (0D = 128 ± 0.929), while fungal richness in the inoculated samples (0D = 32 ± 0.539) was higher than in spontaneous samples (0D = 19 ± 0.917). We identified bacterial groups like Lactobacillus, Leuconostoc, Pediococcus and the Saccharomyces yeast shared in ferments managed with different practices; these organisms are commonly related to the quality of the fermentation process. We identified that clay pots, where spontaneous fermentation is carried out, have an outstanding diversity of fungal and bacterial richness involved in fermentation, being valuable reservoirs of microorganisms for future fermentations. The inoculums displayed the lowest richness and diversity of bacterial and fungal communities suggesting unconscious selection on specific microbial consortia. The beta diversity analysis identified an overlap in microbial communities for both types of fermentation practices, which might reflect a shared composition of microorganisms occurring in the Opuntia streptacantha substrate. The variation in the spontaneous bacterial community is consistent with alpha diversity data, while fungal communities showed less differences among treatments, probably due to the high abundance and dominance of Saccharomyces. This information illustrates how traditional management guides selection and may drive changes in the microbial consortia to produce unique fermented beverages through specific fermentation practices. Although further studies are needed to analyze more specifically the advantages of each fermentation type over the quality of the product, our current analysis supports the role of traditional knowledge driving it and the relevance of plans for its conservation.