Effect of bioaugmentation on biochemical characterisation and microbial communities in Daqu using Bacillus , Saccharomycopsis and Absidia

Changes of microbial communities and metabolites in the fermentation of persimmon vinegar by bioaugmentation fermentation

To evaluate the effects of bioaugmentation fermentation inoculated with one ester-producing strain (Wickerhamomyces anomalus ZX-1) and two strains of lactic acid bacteria (Lactobacillus plantarum CGMCC 24035 and Lactobacillus acidophilus R2) for improving the flavor of persimmon vinegar, microbial community, flavor compounds and metabolites were analyzed. The results of microbial diversity analysis showed that bioaugmentation fermentation significantly increased the abundance of Lactobacillus, Saccharomyces, Pichia and Wickerhamomyces, while the abundance of Acetobacter, Apiotrichum, Delftia, Komagataeibacter, Kregervanrija and Aspergillus significantly decreased. After bioaugmentation fermentation, the taste was softer, and the sensory irritancy of acetic acid was significantly reduced. The analysis of HS-SPME-GC-MS and untargeted metabolomics based on LC-MS/MS showed that the contents of citric acid, lactic acid, malic acid, ethyl lactate, methyl acetate, isocitrate, acetoin and 2,3-butanediol were significantly increased. By multivariate analysis, 33 differential metabolites were screened out to construct the correlation between the differential metabolites and microorganisms. Pearson correlation analysis showed that methyl acetate, ethyl lactate, betaine, aconitic acid, acetoin, 2,3-butanediol and isocitrate positively associated with Wickerhamomyces and Lactobacillus. The results confirmed that the quality of persimmon vinegar was improved by bioaugmentation fermentation.

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.

Insight investigation into the response pattern of microbial assembly succession and volatile profiles during the brewing of sauce-flavor baijiu based on bioaugmentation

To improve the flavor profile and sensory quality of baijiu, the utilization of bioaugmented fermentation inoculated with functional microbiota normally serves as an effective method for directional regulation during the baijiu fermentation process. In this study, a systematic analysis of the succession patterns and volatile flavor compound profiles of microbial communities was carried out by high-throughput sequencing and solid-phase microextraction gas chromatography-mass spectrometry, respectively. The results demonstrated that the Saccharomyces cerevisiae YS222-related bioaugmentation clearly altered the microbial composition, particularly the assembly of bacteria, and promoted the quantity of the most volatile flavoring compounds, including alcohols, esters, and pyrazines. In addition, the correlation analysis showed that Saccharomyces and Lactobacillus in the augmented group were the main biomarkers associated with the dynamics of microbial community and greatly contributed to the brewing of sauce-flavor baijiu, which congruent with the outcomes of the enrichment analysis of integrated metabolic pathway. Thus, this work is beneficial for promoting the quality of baijiu and will serve as a useful reference for clarifying the possible mechanism of augmented fermentation on flavor development.

Microbial interactions from a new perspective: reinforcement learning reveals new insights into microbiome evolution

MOTIVATION

Microbes are essential part of all ecosystems, influencing material flow and shaping their surroundings. Metabolic modeling has been a useful tool and provided tremendous insights into microbial community metabolism. However, current methods based on flux balance analysis (FBA) usually fail to predict metabolic and regulatory strategies that lead to long-term survival and stability especially in heterogenous communities.

RESULTS

Here, we introduce a novel reinforcement learning algorithm, Self-Playing Microbes in Dynamic FBA, which treats microbial metabolism as a decision-making process, allowing individual microbial agents to evolve by learning and adapting metabolic strategies for enhanced long-term fitness. This algorithm predicts what microbial flux regulation policies will stabilize in the dynamic ecosystem of interest in the presence of other microbes with minimal reliance on predefined strategies. Throughout this article, we present several scenarios wherein our algorithm outperforms existing methods in reproducing outcomes, and we explore the biological significance of these predictions.

AVAILABILITY AND IMPLEMENTATION

The source code for this article is available at: https://github.com/chan-csu/SPAM-DFBA.

Effect of inoculated Daqu on the spontaneous fermentation of Chinese liquor

Inoculated fermentation is widely used to improve the efficiency and quality of food production. However, it is still unclear how the inoculated multi-species starters influence food fermentation. Here we prepared two different types of Daqu, with/without the inoculation of Bacillus licheniformis in spontaneous Daqu fermentation, and studied their effects on liquor fermentation. These two types of Daqu were different in microbial community, and the inoculated Daqu had significantly higher relative abundance of Bacillus (69.2%) and lower relative abundance of Lactobacillus (3.2%) than those of Daqu without inoculation (Bacillus, 13.5%; Lactobacillus, 14.0%). After using with these two types of Daqu, metatranscriptomic analysis revealed that Kazachstania, Naumovozyma, Saccharomyces, Nakaseomyces and Lactobacillus were the transcriptional active genera during liquor fermentation. The transcription of Lactobacillus decreased on days 10 and 20 in liquor fermentation with the inoculated Daqu. The transcription of Kazachstania, Naumovozyma and Saccharomyces decreased on day 10 but increased on day 20 with the inoculated Daqu. Although lactate dehydrogenase decreased in Lactobacillus, alcohol dehydrogenase, aldehyde dehydrogenase and lactate dehydrogenase increased in Saccharomyces on day 20 in fermentation with inoculated Daqu, it indicated an extended succession of Saccharomyces in liquor fermentation. This would facilitate the increase of ethanol, acetic acid and lactic acid contents in liquor fermentation with inoculated Daqu. This work would be beneficial for improving Chinese liquor fermentation.

Effects of bio-augmented Daqu on microbial community, aroma compounds and physicochemical parameters of fermented grains during the brewing of Chinese special-flavor baijiu

BACKGROUND

Bio-augmented Daqu is used to improve the microbial community and physicochemical parameters of fermented grains, thus affecting the flavor and quality of baijiu. This study investigated the effects of bio-augmented Daqu inoculated with Aspergillus niger NCUF413.1 and Saccharomyces cerevisiae NCUF304.1 on the microbial community, aroma compounds, and physicochemical parameters of fermented grains during special-flavor baijiu brewing.

RESULTS

Compared with the control group (CG), the utilization of starch and production of ethanol in the inoculated group (IG) increased by 3.55% and 12.59%, respectively. The use of bio-augmented Daqu changed the bacterial communities. For example, Kroppenstedsia was the dominant bacterial genus (the relative abundance was about 22%) in the CG while Lactobacillus was the main dominant genus (the relative abundance was more than 30%) in the IG on days 20-30. Lactobacillus showed a significant positive correlation with the aroma compounds. The use of bio-augmented Daqu increased the aroma compound content - such as the ethyl heptanoate and ethyl hexanoate content.

CONCLUSION

The addition of bio-augmented Daqu with A. niger and S. cerevisiae could change microbial communities, resulting in an increase in the yield of ethanol and the aroma compound content of fermented grains, thus improving the quality of baijiu. © 2022 Society of Chemical Industry.

Mechanism of Enhancing Pyrazines in Daqu via Inoculating Bacillus licheniformis with Strains Specificity

Despite the importance of pyrazines in Baijiu flavor, inoculating functional strains to increase the contents of pyrazine in Daqu and how those interact with endogenic communities is not well characterized. The effects of inoculating Bacillus licheniformis with similar metabolic capacity on pyrazine and community structure were assessed in the Daqu complex system and compared with traditional Daqu. The fortification strategy increased the volatile metabolite content of Daqu by 52.40% and the pyrazine content by 655.99%. Meanwhile, results revealed that the pyrazine content in Daqu inoculated isolate J-49 was 2.35-7.41 times higher than isolate J-41. Both isolates have the almost same capability of 2,3-butanediol, a key precursor of pyrazine, in pure cultured systems. Since the membrane fatty acids of isolate J-49 contain unsaturated fatty acids, it enhances the response-ability to withstand complex environmental pressure, resulting in higher pyrazine content. PICRUSt2 suggested that the increase in pyrazine was related to the enzyme expression of nitrogen metabolism significantly increasing, which led to the enrichment of NH4⁺ and 2,3-butanediol (which increased by 615.89%). These results based on multi-dimensional approaches revealed the effect of functional bacteria enhancement on the attribution of Daqu, laid a methodological foundation regulating the microbial community structure and enhanced the target products by functional strains.

Applications and prospects of the automation of compound flavor baijiu production by solid-state fermentation

Baijiu, the national liquor of China, is produced using traditional solid-state fermentation (SSF). SSF automation during compound flavor baijiu (CFB) production can considerably reduce labor intensity and required manpower, improve the working environment, decrease costs, and increase efficiency. The approaches for SSF automation in CFB production can provide a reference for the automation of SSF in other industries. Therefore, this review compares the traditional and automated processes for jiuqu starter production, SSF, and solid-state distillation during baijiu brewing. Furthermore, specific applications of automation technology and equipment are summarized for each process. The problems and challenges associated with the automation of the process are then detailed and future development directions are proposed. Thus, this review provides an overall introduction to and insight into the developments and challenges in the automation of the CFB brewing process, helping to promote automation in the brewing of other baijiu flavor classes and SSF products.

Biocontrol of Geosmin Production by Inoculation of Native Microbiota during the Daqu-Making Process

Geosmin produced by Streptomyces can cause an earthy off-flavor at trace levels, seriously deteriorating the quality of Chinese liquor. Geosmin was detected during the Daqu (Chinese liquor fermentation starter)-making process, which is a multi-species fermentation process in an open system. Here, biocontrol, using the native microbiota present in Daqu making, was used to control the geosmin contamination. Six native strains were obtained according to their inhibitory effects on Streptomyces and then were inoculated into the Daqu fermentation. After inoculation, the content of geosmin decreased by 34.40% (from 7.18 ± 0.13 μg/kg to 4.71 ± 0.30 μg/kg) in the early stage and by 55.20% (from 8.86 ± 1.54 μg/kg to 3.97 ± 0.78 μg/kg) in the late stage. High-throughput sequencing combined with an interaction network revealed that the fungal community played an important role in the early stage and the correlation between Pichia and Streptomyces changed from the original indirect promotion to direct inhibition after inoculation. This study provides an effective strategy for controlling geosmin contamination in Daqu via precisely regulating microbial communities, as well as highlights the potential of biocontrol for controlling off-flavor chemicals at trace levels in complex fermentation systems.

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.

Structural Characteristics and Formation Mechanism of Microbiota Related to Fermentation Ability and Alcohol Production Ability in Nongxiang Daqu

Fermentation ability and alcohol production ability are important quality indicators of Chinese liquor Daqu, reflecting microbial growth and metabolic capacity and ethanol production capacity of Daqu microbiota, respectively. However, information on the microbial community related to the fermentation ability and alcohol production ability is unclear. In this study, fermentation functional microbiota (FFM) and alcohol functional microbiota (AFM) were obtained by correlating fermentation ability and alcohol production ability with Daqu microbiota. FFM and AFM consisted of 50 and 49 genera, respectively, which were basically the same at the phylum level but differed at the genus level. Correlation analysis showed that FFM and AFM were mainly affected by moisture, acidity, and humidity in the early stage of Daqu fermentation, and oxygen content was a critical factor for microbial succession in the middle stage of fermentation. FFM and AFM had commensal or synergistic interactions with multiple microbes. Function predictions indicated that fermentation functional bacterial microbiota was active in product synthesis and transport-related metabolic functions, and alcohol functional bacterial microbiota was very active in raw material utilization and its own metabolic synthesis. This study reveals the structural characteristics and formation mechanism of FFM and AFM, which is important for control of Daqu quality.

Effects of Different Daqu on Microbial Community Domestication and Metabolites in Nongxiang Baijiu Brewing Microecosystem

The quality and yield of the fresh Baijiu mainly depend on the activity of pit mud (PM) and the quality of Daqu. However, the cultivation of PM is a long-term process, and high-quality Daqu can change the community structure of fermented grain (FG) and accelerate the evolution of PM communities. The present research aimed to investigate the four different types of Daqu on the FG-fermenting microbial community structure and metabolites and their interphase interactions with PM. These results show that Kroppenstedtia in the bacterial community of Taikong Daqu (TK) was positively correlated with ethyl caproate, which significantly increased the content of FG volatile metabolites, especially lipid components, and facilitated the accelerated evolution of Methanobacteriales and Methanosarcinales in PM. Bacillus has a high relative abundance in Qianghua Daqu (QH), which shows obvious advantages to improving the alcoholic strength of FG and contributing to increasing the abundance of Methanomicrobiales in PM. Qianghua and traditional-mixed Daqu (HH) have a similar bacterial composition to QH and a similar fungal composition to traditional Daqu (DZ), and thus also showed the advantage of increased yield, but the volatile flavor metabolites produced were not as dominant as DZ. β-diversity analysis showed that in TK fermentation systems, FG is more likely to domesticate the structure of PM microorganisms. These results indicated that the interaction between microbial communities in Baijiu fermentation niches was significantly influenced by different Daqu. It can not only enhance the key volatiles in FG but also accelerate the evolving direction of the community in PM. Daqu fortified by functional genera or microbiota can evolve a community structure more suitable for Baijiu fermentation. The microbiota composition and interaction between the communities in both Daqu and PM significantly impacts the yield and quality of the base liquor.

Analysis of microbial community, physiochemical indices, and volatile compounds of Chinese te-flavor baijiu daqu produced in different seasons

BACKGROUND

Chinese te-flavor baijiu (CTF), the most famous Chinese baijiu in Jiangxi province, China, is made from a unique daqu. Its characteristic style is closely related to the daqu used for fermentation. However, current studies on the effects of different production seasons on microbial communities, physicochemical indices, and volatile compounds in CTF daqu are very rare.

RESULTS

The relationships of microbial communities, physicochemical indices, and volatile compounds in CTF daqu produced in summer (July and August) and autumn (September and October) were studied. The results of Illumina MiSeq sequencing indicated that there was greater bacterial diversity in the CTF daqu-7 (produced in July) and CTF daqu-8 (produced in August) and greater fungal diversity in the CTF daqu-9 (produced in September) and CTF daqu-10 (produced in October). The physicochemical indices of CTF daqu produced in different seasons were significantly different. It was determined that CTF daqu-9 had the highest esterification and liquefaction abilities. A total of 44 volatile compounds, including alcohols, esters, aldehydes, and ketones were identified in CTF daqu produced during different seasons. Among them, CTF daqu-9 had the greatest alcohol content.

CONCLUSION

September (early autumn) is the best production period for CTF daqu. The results of the study provide a theoretical basis for the standardized and uniform production of Chinese baijiu. © 2021 Society of Chemical Industry.

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

Traditional fermented foods are usually produced by spontaneous fermentation with multiple microorganisms. Environmental factors play important roles in microbial succession. However, it is still unclear how the processing parameters regulate the microbiota during fermentation. Here, we reveal the effects of processing parameters on the core microbiota in spontaneous fermentation of Chinese liquor starter. Rhizopus, Pichia, Wickerhamomyces, Saccharomycopsis, Aspergillus and Saccharomyces were identified as core microbiota using amplicon sequencing and metaproteomics analysis. Fermentation moisture gradually decreased from 34.8% to 14.2%, and fermentation temperature varied between 17.0 °C and 35.3 °C during the fermentation. Mantel test showed that fermentation moisture (P < 0.001) and fermentation temperature (P < 0.05) significantly affected the core microbiota. Moreover, structural equation modelling analysis indicated that fermentation moisture (P < 0.001) and fermentation temperature (P < 0.001) were respectively influenced by the processing parameters, room humidity and room temperature. The succession of Rhizopus, Pichia, Wickerhamomyces, Saccharomycopsis and Aspergillus were significantly affected by room humidity (P < 0.05), and the succession of Saccharomyces was significantly affected by room temperature (P < 0.001). Further, models were constructed to predict the population of core microbiota by room humidity and room temperature, using Gaussian process regression and linear regression (P < 0.05). This work would be beneficial for regulating microorganisms via controlling processing parameters in spontaneous food fermentations.

Bioaugmentation by Pediococcus acidilactici AAF1-5 Improves the Bacterial Activity and Diversity of Cereal Vinegar Under Solid-State Fermentation

Bioaugmentation technology may be an effective strategy to improve the solid-state fermentation rate and utilization of raw materials for traditional vinegar production. The relationship between bacteria and fermentation process was analyzed to rationally design and perform bioaugmented solid-state fermentation of the Tianjin Duliu mature vinegar (TDMV). Fermentation process was highly correlated with Acetobacter, Lactobacillus, and Pediococcus contents, which were the core functional microorganisms in TDMV fermentation. Pediococcus acidilactici AAF1-5 was selected from 20 strains to fortify the fermentation due to its acidity and thermal tolerance. Bioaugmentation was performed in the upper layer of TDMV fermentation. P. acidilactici AAF1-5 colonized and then spread into the lower layer to improve the fermentation. Result showed that the fermentation period was 5 days less than that of the control. Meanwhile, the non-volatile acid, lactic acid, amino nitrogen, and reducing sugar contents in the bioaugmented TDMV increased by 53%, 14%, 32%, and 36%, respectively, compared with those in the control. Bioaugmentation with P. acidilactici AAF1-5 not only improved the utilization of starch from 79% to 83% but also increased the bacterial community diversity.

Application of Wickerhamomyces anomalus in Simulated Solid-State Fermentation for Baijiu Production: Changes of Microbial Community Structure and Flavor Metabolism

Wickerhamomyces anomalus is conducive to the synthesis of ester compounds in brewing the Chinese liquor Baijiu; esters are crucial for the quality of Baijiu. In this study, simulated solid-state fermentation for Baijiu production was used to explore whether artificial addition of W. anomalus could improve the flavor substance in Baijiu, and the underlying mechanisms. Two experimental groups were studied, in which W. anomalus Y3604 (Group A) and YF1503 (Group B) were added, respectively; in the control group (Group C), no W. anomalus was added. Adding strain Y3604 increased the content of esters in fermentation samples, especially ethyl acetate and ethyl caproate, and reduced the content of higher alcohols. Adding strain YF1503 had little effect on the ester content but decreased the content of higher alcohols. The diversity and abundance of prokaryotic genera in Group A and B samples were similar, but there were some differences compared with Group C. The correlations of genera in Group A or B samples were simple compared with group C. Although the predominant eukaryotic genera in the three groups were consistent, the abundance of each gene varied among groups. Based on our findings, bioaugmentation of Baijiu fermentation with W. anomalus will change the ethyl acetate content and cause changes in the levels of other flavor substances. We suggest that the changes in flavor substances caused by the addition of W. anomalus are mainly due to changes in the microbial community structure that result from the addition of W. anomalus.