Laboratory-scale fermentation and multidimensional screening of lactic acid bacteria from Daqu

Microbial interactions in mixed-species biofilms on the surfaces of Baijiu brewing environments

Environmental microorganisms commonly inhabit dense multispecies biofilms, fostering mutualistic relationships and co-evolution. However, the mechanisms underlying biofilm formation and microbial interactions within the Baijiu fermentation microecosystem remain poorly understood. Hence, the objective of this study was to investigate the composition, structure, and interactions of microorganisms residing in biofilms on environmental surfaces in Baijiu production. The results revealed a shift in the bacteria-fungi interaction network following fermentation, transitioning from a cooperative/symbiotic relationship to a competitive/antagonistic dynamic. Core microbiota within the biofilms comprised lactic acid bacteria (LAB), yeast, and filamentous fungi. From the environmental surface samples, we isolated two strains of LAB (Lactiplantibacillus pentosus EB27 and Pediococcus pentosaceus EB35) and one strain of yeast (Pichia kudriavzevii EF8), all displaying remarkable biofilm formation and fermentation potential. Co-culturing LAB and yeast demonstrated a superior capacity for dual-species biofilm formation compared to mono-species biofilms. The dual-species biofilm displayed a two-layer structure, with LAB in the lower layer and serving as the foundation for the yeast community in the upper layer. The upper layer exhibited a dense distribution of yeast, enhancing aerobic respiration. Metabolic activities in the dual-species biofilm, such as ABC transporter, oxidative phosphorylation, citric acid cycle, sulfur metabolism, glycine, serine, threonine metabolism, lysine degradation, and cysteine and methionine metabolism, showed significant alterations compared to LAB mono-species biofilms. Moreover, bacterial chemotaxis, starch, and sucrose metabolism in the dual-species biofilm exhibited distinct patterns from those observed in the yeast mono-species biofilm. This study demonstrated that a core microbiota with fermentation potential may exist in the form of a biofilm on the surface of a Baijiu brewing environment. These findings provide a novel strategy for employing synthetic stable microbiotas in the intelligent brewing of Baijiu.

Developing defined starter culture for reproducible profile of flavour compound in Chinese xiaoqu baijiu fermentation

Defined starter cultures, containing selected microbes could reduce the complexity of natural starter, are beneficial for controllable food fermentations. However, there are challenges in identifying key microbiota and constructing synthetic microbiota for traditional food fermentations. Here, we aimed to develop a defined starter culture for reproducible profile of flavour compounds, using Chinese Xiaoqu Baijiu fermentation as a case. We classified all microbes into 4 modules using weighted correlation network analysis. Module 3 presented significant correlations with flavour compounds (P < 0.05) and the highest gene abundance related with flavour compound production. 13 dominant species in module 3 were selected for mixed culture fermentation, and each species was individually deleted to analyse the effect on flavour compound production. Ten species, presenting significant effects (P < 0.05) on flavour compound production, were selected for developing the starter culture, including Rhizopus oryzae, Rhizopus microsporus, Saccharomyces cerevisiae, Pichia kudriavzevii, Wickerhamomyces anomalus, Lactobacillus acetotolerans, Levilactobacillus brevis, Weissella paramesenteroides, Pediococcus acidilactici, and Leuconostoc pseudomesenteroides. After optimising the structure of the starter culture, the profile similarity of flavour compounds produced by the starter culture reached 81.88% with that by the natural starter. This work indicated feasibility of reproducible profile of flavour compounds with defined starter culture for food fermentations.

Identification of volatile metabolites produced from levodopa metabolism by different bacteria strains of the gut microbiome

Interspecies pathways in the gut microbiome have been shown to metabolize levodopa, the primary treatment for Parkinson's disease, and reduce its bioavailability. While the enzymatic reactions have been identified, the ability to establish the resulting macromolecules as biomarkers of microbial metabolism remains technically challenging. In this study, we leveraged an untargeted mass spectrometry-based approach to investigate volatile organic compounds (VOCs) produced during levodopa metabolism by Enterococcus faecalis, Clostridium sporogenes, and Eggerthella lenta. We cultured these organisms with and without their respective bioactive metabolites and detected levodopa-induced shifts in VOC profiles. We then utilized bioinformatics to identify significant differences in 2,6-dimethylpyrazine, 4,6-dimethylpyrimidine, and 4,5-dimethylpyrimidine associated with its biotransformation. Supplementing cultures with inhibitors of levodopa-metabolizing enzymes revealed specific modulation of levodopa-associated diazines, verifying their relationship to its metabolism. Furthermore, functional group analysis depicts strain-specific VOC profiles that reflect interspecies differences in metabolic activity that can be leveraged to assess microbiome functionality in individual patients. Collectively, this work identifies previously uncharacterized metabolites of microbe-mediated levodopa metabolism to determine potential indicators of this activity and further elucidate the metabolic capabilities of different gut bacteria.

Deciphering the core microbes and their interactions in spontaneous Baijiu fermentation: A comprehensive review

The spontaneous Baijiu fermentation system harbors a complex microbiome that is highly dynamic in time and space and varies depending on the Jiuqu starters and environmental factors. The intricate microbiota presents in the fermentation environment is responsible for carrying out various reactions. These reactions necessitate the interaction among the core microbes to influence the community function, ultimately shaping the distinct Baijiu styles through the process of spontaneous fermentation. Numerous studies have been conducted to enhance our understanding of the diversity, succession, and function of microbial communities with the aim of improving fermentation manipulation. However, a comprehensive and critical assessment of the core microbes and their interaction remains one of the significant challenges in the Baijiu fermentation industry. This paper focuses on the fermentation properties of core microbes. We discuss the state of the art of microbial traceability, highlighting the crucial role of environmental and starter microbiota in the Baijiu brewing microbiome. Also, we discuss the various interactions between microbes in the Baijiu production system and propose a potential conceptual framework that involves constructing predictive network models to simplify and quantify microbial interactions using co-culture models. This approach offers effective strategies for understanding the core microbes and their interactions, thus beneficial for the management of microbiota and the regulation of interactions in Baijiu fermentation processes.

Screening of a potential probiotic Lactiplantibacillus plantarum NUC08 and its synergistic effects with yogurt starter

This study aims to identify lactic acid bacteria (LAB) isolates possessing physiological characteristics suitable for use as probiotics in yogurt fermentation. Following acid and bile salt tolerance tests, Lactiplantibacillus plantarum (NUC08 and NUC101), Lacticaseibacillus rhamnosus (NUC55 and NUC201), and Lacticaseibacillus paracasei (NUC159, NUC216, and NUC351) were shortlisted based on intraspecies distribution for further evaluation. Their physiological probiotic properties, including transit tolerance, adhesion, autoaggregation, surface hydrophobicity, biofilm formation, and antibacterial activity, were assessed. Principal component analysis indicated that Lactiplantibacillus plantarum NUC08 was the preferred choice among the evaluated strains. Subsequent investigations revealed that co-culturing Lactiplantibacillus plantarum NUC08 with 2 yogurt starter strains resulted in a cooperative and synergistic effect, enhancing the growth of mixed strains and increasing their tolerance to simulated gastric and intestinal conditions. Additionally, when Vibrio harveyi bioluminescent reporter strain was used, the 3 cocultured strains cooperated to induce the activity of a quorum sensing (QS) molecule autoinducer-2 (AI-2), hinting a potential connection between phenotypic traits and QS in the cocultured strains. Importantly, LAB viable counts were significantly higher in yogurt co-fermented with Lactiplantibacillus plantarum NUC08, consistently throughout the storage period. In conclusion, the study demonstrates that the probiotic strain Lactiplantibacillus plantarum NUC08 can be employed in synergy with yogurt starter strains, affirming its potential for use in the development of functional fermented dairy products.

Volatile compounds produced in smoked bacon inoculated with potential spoilage bacteria

BACKGROUND

Volatile organic compounds (VOCs) produced during meat storage are mainly derived from the decomposition of meat components and the metabolism of spoilage bacteria. VOCs produced in sterile bacon model substrate inoculated or un-inoculated with spoilage bacteria, Staphylococcus xylosus (P2), Leuconostoc mesenteroides (P6), Carnobacterium maltaromaticum (P9), Leuconostoc gelidum (P16) and Serratia liquefaciens (P20), previously isolated, were identified by headspace solid-phase microextraction (HS-SPME) coupled with gas chromatography-mass spectrometry (GC-MS). Furthermore, combinations of the strains (Pm) were also obtained.

RESULTS

In total, 54 volatile compounds, including aldehydes, alcohols, phenols, ketones, alkanes, alkanes, organic acids, esters and so forth, were determined after 45 days of storage in bacon inoculated with potential spoilage bacteria using the HS-SPME/GC-MS method. VOC concentrations of alcohols and organic acids in groups inoculated with bacteria were remarkably higher (P < 0.05) compared to that in control samples. Specifically, some VOCs are closely related to the metabolic activity of the inoculated bacterial strains; for example, 2,3-butanediol was associated with P2, P16 and P20, and acetic acid was mainly related to P6 and P9.

CONCLUSION

The results of partial least squares regression indicated that there was a high correlation between the electronic nose sensors and VOCs of smoked inoculated potential spoilage bacteria. These compounds are potentially important for predicting deterioration of smoked bacon. © 2023 Society of Chemical Industry.

Effect of Fortified Inoculation with Indigenous Lactobacillus brevis on Solid-State Fermentation of Light-Flavor Baijiu

Baijiu, one of the world's oldest distilled liquors, is widely consumed globally and has gained increasing popularity in East Asia. However, a comprehensive understanding of the underlying principles behind this traditional liquor product remains elusive. Currently, Baijiu is facing the industrial challenge of modernization and standardization, particularly in terms of food quality, safety, and sustainability. The current study selected a Lactobacillus brevis strain based on experiments conducted to assess its environmental tolerance, enzyme activity, and fermentation performance, and highlight its exceptional fermentation characteristics. The subsequent analysis focused on examining the effects of fortifying the fermentation process of L.brevis on key microbiotas, physicochemical parameters, and volatile profiles. The qPCR results revealed that the inoculated L. brevis strategically influenced the the composition of the dominant microbial communities by promoting mutual exclusion, ultimately leading to improved controllability of the fermentation process. Moreover, the metabolism of the inoculated L. brevis provided more compounds for the formation of flavor profiles during fermentation (the content of ethyl acetate was increased to 57.76 mg/kg), leading to a reduction in fermentation time (from 28 d to 21 d). These findings indicate promising potential for the application of the indigenous strain in Baijiu production.

Exploring the controllability of the Baijiu fermentation process with microbiota orientation

Product quality and stability improvement is important for development of the Baijiu industry. Generally, Baijiu brewing is carried out in a spontaneous fermentation system mediated by microbiota. Thus, complexity and instability are major features. Due to the insufficient understanding of the mechanism for producing Baijiu, the precise control of the fermentation progress has still not been realized, ultimately affecting product quality and stability. The flavor of Baijiu is the most important factor in determining its quality and is formed by microbiota under the driving force of various physicochemical parameters, such as moisture, acidity, and temperature. Therefore, exploring the association among microbiota (core), physicochemical factors (reference) and flavor compounds (target) has become a key point to clarify the formation mechanism for the flavor quality of Baijiu. Daqu fermentation and liquor fermentation are the two major stages of Baijiu brewing. Daqu, distillers' grains, and pit mud, as the most important fermentation substrates of the microbiota respectively, provide a large number of functional microorganisms related to the flavor components. To this end, we reviewed the relevant research progress of microbiota diversity in different fermentation substrates and the interaction mechanisms among microbiota, physicochemical parameters, and flavor components in this paper. Moreover, a research hypothesis of precise control of the Baijiu fermentation process by building fermentation models based on this is proposed. The key point for this idea is the identification of core microbiota closely associated with the formation of key flavor components by multi-omics technology and the acquisition of culturable strains. With this foundation, fermentation models suitable for different brewing environments will be established by constructing synthetic microbiota, designing mathematical models, and determining key fermentation model parameters. The ultimate goal will be to effectively improve the quality and stability of Baijiu products through model regulation.

Non-gene-editing microbiome engineering of spontaneous food fermentation microbiota-Limitation control, design control, and integration

Non-gene-editing microbiome engineering (NgeME) is the rational design and control of natural microbial consortia to perform desired functions. Traditional NgeME approaches use selected environmental variables to force natural microbial consortia to perform the desired functions. Spontaneous food fermentation, the oldest kind of traditional NgeME, transforms foods into various fermented products using natural microbial networks. In traditional NgeME, spontaneous food fermentation microbiotas (SFFMs) are typically formed and controlled manually by the establishment of limiting factors in small batches with little mechanization. However, limitation control generally leads to trade-offs between efficiency and the quality of fermentation. Modern NgeME approaches based on synthetic microbial ecology have been developed using designed microbial communities to explore assembly mechanisms and target functional enhancement of SFFMs. This has greatly improved our understanding of microbiota control, but such approaches still have shortcomings compared to traditional NgeME. Here, we comprehensively describe research on mechanisms and control strategies for SFFMs based on traditional and modern NgeME. We discuss the ecological and engineering principles of the two approaches to enhance the understanding of how best to control SFFM. We also review recent applied and theoretical research on modern NgeME and propose an integrated in vitro synthetic microbiota model to bridge gaps between limitation control and design control for SFFM.

Role of bacterial community succession in flavor formation during Sichuan sun vinegar grain (Cupei) fermentation

Sichuan sun vinegar (SSV) is a traditional Chinese vinegar with a unique flavor and it is fermented with bran as the main raw material. In the present study, we explored the bacterial community succession in fermented grains (Cupei) during SSV production. High-throughput sequencing results showed that bacterial community richness and diversity peaked on day 7 of fermentation. Lactobacillus and Acetobacter were the dominant bacteria throughout the fermentation process. However, Acetobacter, Cupriavidus, Sphingomonas, Pelomonas, and Lactobacillus were the most abundant genera in the late phase of fermentation on day 17. The boundaries of trilateral co-fermentation were determined through cluster analysis. Days 1-3 were considered the early fermentation stage (starch saccharification), days 5-11 were the middle fermentation stage (alcoholic fermentation), and days 13-17 represented the late fermentation stage (acetic acid fermentation). Changes in flavor compounds during Cupei fermentation were subsequently analyzed and a total of 86 volatile compounds, 9 organic acids, and 17 amino acids were detected. Although acetic acid, lactic acid, alcohols, and esters were the main metabolites, butyrate was also detected. Correlation analysis indicated that 20, 21, and 28 microorganisms were positively correlated with the abundance of amino acids, organic acids, and volatile flavor compounds, respectively. We further explored the microbial and metabolic mechanisms associated with the dominant volatile flavor compounds during SSV fermentation. Collectively, the findings of the current study provide detailed insights regarding the fermentation mechanisms of SSV, which may prove relevant for producing high-quality fermented products.

Analysis of the Microbial Community Structure and Volatile Metabolites of JIUYAO in Fangxian, China

JIUYAO is an important saccharification starter in the production of huangjiu and is also an important source of flavor. In this study, the microbial community structure of JIUYAO from Fangxian was studied by high-throughput sequencing (HTS) technology for the first time. The volatile flavor compounds of the JIUYAO metabolites were also analyzed by headspace solid-phase microextraction combined with full two-dimensional gas chromatography-mass spectrometry (HS-SPME-GC×GC/MS) for the first time. The results showed that there were 15 dominant bacterial genera, including Weissella, Pediococcus, unclasssified_k_norank_d_Bacteria, Lactobacillus, Leuconostoc, etc. Thirteen species of dominant fungi included Wickerhamomyces, Saccharomycopsis, Rhizopus, etc. The different samples of JIUYAO were similar in their microbial species, but the number of species was significantly different. A total of 191 volatile flavor compounds (VFCs) were detected, among which esters, alcohols, acids, and alkenes were the main flavor compounds, and 21 terpenoids were also detected. In addition, the functional prediction of micro-organisms in JIUYAO revealed that global and overview maps, amino acid metabolism, and carbohydrate metabolism were the dominant categories. Through correlation analysis, 538 potential correlations between the dominant micro-organisms and the different flavor compounds were obtained. This study revealed the interactions between the micro-organisms and the volatile metabolites in JIUYAO, which provided reliable data for the analysis of the microbial community structure of Fangxian JIUYAO and provided theoretical support for the quality evaluation of JIUYAO.

The Influence of Seasons on the Composition of Microbial Communities and the Content of Lactic Acid during the Fermentation of Fen-Flavor Baijiu

During the fermentation of Fen-flavor Baijiu, the number of lactic acid bacteria is high in summer, resulting in excessive lactic acid and an unpleasant astringent taste. Thus, it is necessary to identify the critical influence factors for the formation of lactic acid and the composition of the microbial community in the fermented grains during the brewing process of Fen-flavor Baijiu in cold and hot seasons using HPLC and high-throughput sequencing technology. The results suggest that Lactobacillus acetotolerans is the key microorganism causing different contents of lactic acid in fermented grains and that Lactobacillus plantarum is a favorable factor for acid production in the fermentation process during hot seasons. Twelve lactic-acid-producing strains were isolated from the fermented grains at the latter stage of fermentation, and the analysis of these strains showed that the Lactobacillus plantarum LP strain has the strongest capacity for lactic acid production and the Lacticaseibacillus rhamnosus LR strain has the strongest capacity for acid production, respectively. In addition, the Lentilactobacillus hilgardii LH strain has the characteristics of both acid and alcohol resistance. The results obtained from this study provide a reference for reducing the content of lactic acid in summer and have potential value for further improving the quality of Fen-flavor Baijiu.

Taorong-type Baijiu starter: Analysis of fungal community and metabolic characteristics of middle-temperature Daqu and high-temperature Daqu

To study the difference between the fungal community compositional and fragrance components in medium- and high-Temperature Taorong-type Baijiu Daqu. The microbial communities and fragrance components of Taorong-type Baijiu Daqu were analyzed using high-throughput sequencing (HTS) and headspace-solid-phase microextraction-gas chromatography-mass spectrometry (HS-SPME-GC-MS). With an abundance at the phylum and genus levels ≥0.01% as the threshold, 3 phyla, Mucoromycota, Ascomycota, and Basidiomycota, were found in both medium- and high-temperature Daqu, but their abundances differed. At the genus level, 15 and 13 genera were recognized. Rhizopus (72.40%) and Thermomyces (53.32%) accounted for the most significant proportions in medium-temperature and high-temperature Daqu, respectively. Medium-temperature Daqu and high-temperature Daqu were found to have 40 and 29 fragrance components, respectively and contained the highest proportions of pyrazines (53.12%) and acids (32.68%). Correlation analyses between microbes and fragrance components showed that Aspergillus, Hyphopichia, Trichosporon, Alternaria were all highly and positively correlated with pyrazines, but the dominant fungal communities were highly correlated with only a few individual acid compounds but not with acid compounds overall. The unique Daqu -making process and environment lead to these differences.

A systematic, complexity-reduction approach to dissect the kombucha tea microbiome

One defining goal of microbiome research is to uncover mechanistic causation that dictates the emergence of structural and functional traits of microbiomes. However, the extraordinary degree of ecosystem complexity has hampered the realization of the goal. Here, we developed a systematic, complexity-reducing strategy to mechanistically elucidate the compositional and metabolic characteristics of microbiome by using the kombucha tea microbiome as an example. The strategy centered around a two-species core that was abstracted from but recapitulated the native counterpart. The core was convergent in its composition, coordinated on temporal metabolic patterns, and capable for pellicle formation. Controlled fermentations uncovered the drivers of these characteristics, which were also demonstrated translatable to provide insights into the properties of communities with increased complexity and altered conditions. This work unravels the pattern and process underlying the kombucha tea microbiome, providing a potential conceptual framework for mechanistic investigation of microbiome behaviors.

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.

Study on the Effect of Key Genes ME2 and adhE during Luzhou-flavor Baijiu Brewing

Luzhou-flavor baijiu (LFB) is brewed by the combined action of various microorganisms, and its flavor is affected by the microbial community and the genes they express, but which genes are the key ones during LFB brewing is less clear. Based on our previous studies the genes ME2 and adhE were identified as key genes, but which role they play was also unknown. In this study functional microorganisms were screened based on the key genes ME2 and adhE, and they were identified to be Rummeliibacillus suwonensis, Clostridium tyrobutyricum and Lactobacillus buchneri. Then simulated fermentation experiments were carried out with the functional microorganisms, and during the fermentation process expression of the key genes and the amounts of the main flavors were detected to analyze the role of the key genes. The results showed that the key gene ME2 was significantly positively correlated with the contents of the main acids, however the key gene adhE and the formation of the main esters in the LFB brewing process was a significant positive correlation. This study verified the two key genes ME2 and adhE complement each other in the LFB brewing process, playing an important role in promoting the formation of flavor substances, and are very beneficial to improve the quality of LFB.

Microbial Diversity and Metabolites Dynamic of Light-Flavor Baijiu with Stacking Process

Stacking is a widely used method of microbial enrichment in the field of fermentation and is traditionally used to promote flavor in Chinese sauce-flavor Baijiu; however, its precise mechanism is unknown. This study assessed the fermentation process of light-flavor Baijiu with the simplest microbial source. After comparing differences in the microbial composition of different kinds of Daqu, a high-temperature Daqu with a microbial composition that significantly differs from light-flavor Daqu was selected for stacking. The physical and chemical indicators, microbial community composition, and metabolite profiles during the fermentation process were tracked, and the total ester content in Baiju was significantly higher with stacking than Baijiu without stacking. The dominant bacteria during stacking fermentation were Bacillus and Enterococcus, while Lactobacillus was the dominant bacteria during middle and late fermentation periods. Low levels of Lactobacillus and Pichia in Daqu were screened and enriched during the stacking process, while the glucose and acetate content significantly increased. Flavor compounds such as esters and acids were positively correlated with dominant genera such as Lactobacillus, Bacillus, and Pichia. Stacking provides microorganisms for environmental screening, which regulates the microbial community structure and produces various metabolites and precursors of flavor substances to fully saccharify and promote the production of flavor substances. Stacking during the production of light-flavor Baijiu can help regulate the fermentation process and improve Baijiu quality.