Source tracking of prokaryotic communities in fermented grain of Chinese strong-flavor liquor

Metaproteomics insights into traditional fermented foods and beverages

Traditional fermented foods and beverages (TFFB) are important dietary components. Multi-omics techniques have been applied to all aspects of TFFB research to clarify the composition and nutritional value of TFFB, and to reveal the microbial community, microbial interactions, fermentative kinetics, and metabolic profiles during the fermentation process of TFFB. Because of the advantages of metaproteomics in providing functional information, this technology has increasingly been used in research to assess the functional diversity of microbial communities. Metaproteomics is gradually gaining attention in the field of TFFB research because it can reveal the nature of microorganism function at the protein level. This paper reviews the common methods of metaproteomics applied in TFFB research; systematically summarizes the results of metaproteomics research on TFFB, such as sauces, wines, fermented tea, cheese, and fermented fish; and compares the differences in conclusions reached through metaproteomics versus other omics methods. Metaproteomics has great advantages in revealing the microbial functions in TFFB and the interaction between the materials and microbial community. In the future, metaproteomics should be further applied to the study of functional protein markers and protein interaction in TFFB; multi-omics technology requires further integration to reveal the molecular nature of TFFB fermentation.

Temperature-Induced Annual Variation in Microbial Community Changes and Resulting Metabolome Shifts in a Controlled Fermentation System

We are rapidly increasing our understanding on the spatial distribution of microbial communities. However, microbial functioning, as well as temporal differences and mechanisms causing microbial community shifts, remains comparably little explored. Here, using Chinese liquor fermentation as a model system containing a low microbial diversity, we studied temporal changes in microbial community structure and functioning. For that, we used high-throughput sequencing to analyze the composition of bacteria and fungi and analyzed the microbially derived metabolome throughout the fermentation process in all four seasons in both 2018 and 2019. We show that microbial communities and the metabolome changed throughout the fermentation process in each of the four seasons, with metabolome diversity increasing throughout the fermentation process. Across seasons, bacterial and fungal communities as well as the metabolome driven by 10 indicator microorganisms and six metabolites varied even more. Daily average temperature in the external surroundings was the primary determinant of the observed temporal microbial community and metabolome changes. Collectively, our work reveals critical insights into patterns and processes determining temporal changes of microbial community composition and functioning. We highlight the importance of linking taxonomic to functional changes in microbial ecology to enable predictions of human-relevant applications.IMPORTANCE We used Chinese liquor fermentation as a model system to show that microbiome composition changes more dramatically across seasons than throughout the fermentation process within seasons. These changes translate to differences in the metabolome as the ultimate functional outcome of microbial activity, suggesting that temporal changes in microbiome composition are translating into functional changes. This result is striking as it suggests that microbial functioning, despite controlled conditions in the fermentors, fluctuates over season along with external temperature differences, which threatens a reproducible food taste. As such, we believe that our study provides a stepping-stone into novel taxonomy-functional studies that promote future work in other systems and that also is relevant in applied settings to better control surrounding conditions in food production.

Analyzing bacterial community in pit mud of Yibin Baijiu in China using high throughput sequencing

“Yibin Baijiu” (YB) is a special Chinese strong-aroma Baijiu (CSAB) that originated in Yibin, a city in western China. YB is fermented in cellars lined with pit mud (PM), the microbiota in which may affect YB quality. In this study, high throughput sequencing of the 16S rRNA gene was used to demonstrate the bacterial community structure and diversity in PM of YB. In addition, the physicochemical characteristics of PM were also analyzed, including moisture content, pH, and available phosphorous, ammonia nitrogen, and humic acid levels. Results showed that Firmicutes was the dominant phylum in all PM samples with abundance > 70.0%, followed by Euryarchaeota (11.3%), Bacteroidetes (6.5%), Synergistetes (3.0%), Actinobacteria (1.4%), and Proteobacteria (1.2%). Furthermore, 14 different genera with average relative abundance of > 1% were detected. The Chao1 and Shannon indexes did not vary significantly between the sub-layer and middle-layer PM (P > 0.05). However, Linear discriminant analysis Effect Size (LEfSe) analysis showed that the relative abundance of Lactobacillus in the sub-layer PM was significantly higher than in middle-layer PM. pH differed significantly (P < 0.05) between the two groups. Canonical correspondence analysis revealed that bacterial community in PM correlated significantly with available phosphorous content and pH. Our study provides basic data for further elucidating the diversity of microbiota in the PM of YB and the potential mechanism of Baijiu production.

Directional design of a starter to assemble the initial microbial fermentation community of baijiu

Tetramethylpyrazine (TTMP) is an important aroma compound in the sesame-flavored Chinese liquor, baijiu. Similar to other traditional spontaneously fermented foods, it is difficult to directionally increase the key aroma compound in situ fermentation system of baijiu without changing its sensory profile. The assembly of the starting microbial community for fermentation by using a functional starter provides a promising solution which needs careful manipulations. This study aimed to increase TTMP concentration in baijiu using the functional starter inoculated with the indigenous strain B. amyloliquefaciens XJB-104 with high TTMP production ability. After inoculation, the relative abundance of Bacillus in the initial stage of fermentation increased from 82.14% to 88.47%. The TTMP concentration increased by about 26 and 24-fold in the fermented grains (zaopei) and baijiu respectively compared with controls. Moreover, the quality of baijiu was improved according to sensory analyses. In addition, correlation analysis confirmed that the increased TTMP content in baijiu was due to the successful assembly of the initial fermentation microbiota after the inoculation of B. amyloliquefaciens.

Major Metabolites and Microbial Community of Fermented Black Glutinous Rice Wine With Different Starters

Black glutinous rice wine (BGRW) is a traditional Chinese rice wine that is brewed using multiple strains. However, the roles of these microorganisms, particularly their contributions to aroma formation, are poorly understood. Accordingly, the main goal of this study was to determine the microbial communities and major metabolites of different traditional fermentation starters. Anshun (AS) starter and Xingyi (XY) starter were used for BGRW to provide insight into their potential contributions to the variation in flavor and aroma. High-throughput sequencing of the microbial community using the Illumina MiSeq platform revealed significant differences during fermentation between the two starter groups. Pediococcus, Leuconostoc, and Bacillus were the dominant bacterial genera in the AS group, whereas Leuconostoc, Pediococcus, and Gluconobacter were the dominant genera in the XY group. In addition, Rhizopus, Saccharomyces, and Saccharomycopsis were the predominant fungal genera detected in both samples. The major metabolites in the two groups were identified by high-performance liquid chromatography and headspace-solid-phase microextraction gas chromatography–mass spectrometry. A total of seven organic acids along with 47 (AS) and 43 (XY) volatile metabolites were detected, among which lactic acid was the primary organic acid, and esters were the largest group in both types of wine. Principal components analysis further revealed significant differences in the dynamic succession of metabolites between the two samples. Correlation analysis showed that 22 and 17 microorganisms were strongly correlated with the production of major metabolites in AS and XY, respectively. Among them, Pediococcus, Leuconostoc, Lactobacillus, Lactococcus, and Streptococcus were shown to play crucial roles in metabolite synthesis. Overall, this study can provide a valuable resource for the further development and utilization of starters to improve the aromatic quality of BGRW.

Correlation between autochthonous microbial communities and key odorants during the fermentation of red pepper (Capsicum annuum L.)

High-throughput sequencing and gas chromatography-mass spectrometry (GC-MS) were used to investigate changes in bacterial and fungal communities and volatile flavor compounds during a 32-day fermentation process of red pepper (Capsicum annuum L.). Key odorants were identified by olfactometry combined with GC-MS. Sixteen volatile compounds differed significantly after fermentation, including seven odorants. After fermentation, 1-butanol, 3-methyl-, acetate, phenol, 4-ethyl-2-methoxy-, octanoic acid, ethyl ester, styrene and 2-methoxy-4-vinylphenol were the key odorants, producing a flavor described as peppery, fruity, sour, and spicy. The correlation between microorganisms and odorants in the fermentation was studied and 18 odorants significantly correlated with the core microbial communities in the fermented samples. For further analysis, strains of seven genera were isolated and correlation analysis by O2PLS indicated that Aspergillus, Bacillus, Brachybacterium, Microbacterium and Staphylococcus were highly correlated with the flavor formation. These findings would help to understand the fermentation mechanism of fermented red pepper flavor formation.

Synergistic Effect of Multiple Saccharifying Enzymes on Alcoholic Fermentation for Chinese Baijiu Production

Chinese Jiuqu (fermentation starter) provides saccharifying enzymes for baijiu (Chinese liquor) fermentation, which undergoes a simultaneous saccharification and fermentation process. However, the key saccharifying enzymes associated with alcoholic fermentation from Jiuqu and their effects on ethanol production remain poorly understood. In this study, we identified 51 carbohydrate hydrolases in baijiu fermentation by metaproteomics analysis. Through source-tracking analysis, approximately 80% of carbohydrate hydrolases in the baijiu fermentation were provided by Jiuqu Among these enzymes, alpha-amylase (EC 3.2.1.1) and glucoamylase (EC 3.2.1.3), from Aspergillus, Rhizomucor, and Rhizopus, were positively related to starch hydrolysis and ethanol production, indicating that they were the key saccharifying enzymes associated with alcoholic fermentation in the baijiu fermentation. Moreover, a combined mixture of alpha-amylase and glucoamylase (in a ratio of 1:6, wt/wt) enhanced ethanol production in a simulative baijiu fermentation under laboratory conditions. This result revealed a synergistic effect of multiple saccharifying enzymes on ethanol production in baijiu fermentation. Our study provides a potential approach to improve the efficiency of saccharification and alcoholic fermentation by optimizing the profile of saccharifying enzymes for fermentation of baijiu and other beverages.IMPORTANCE Jiuqu starter provides enzymes to the simultaneous saccharification and fermentation process of baijiu (Chinese liquor) production; however, the key saccharifying enzymes associated with alcoholic fermentation from Jiuqu and their effects on ethanol production remain unclear. We confirmed that Jiuqu was the main source of carbohydrate hydrolases for baijiu fermentation and identified two types of saccharifying enzymes from multiple microbes as the key enzymes associated with alcoholic fermentation. Moreover, a proper combination of multiple saccharifying enzymes could enhance ethanol production in baijiu fermentation. This combination provides an approach to optimize the profile of saccharifying enzymes for enhancing ethanol production in baijiu and other food fermentations.

Effects of aging on the quality of roasted sesame-like flavor Daqu

Background

Daqu, the saccharification, fermentation, and aroma-producing agents for Baijiu brewing, is prepared using a complex process. Aging is important for improving the quality of Daqu, but its impact has rarely been studied. This study investigated changes in the physicochemical properties, flavor compounds, and microbial communities during aging of Daqu with a roasted sesame-like flavor.

Results

The physicochemical properties changed continuously during aging to provide a high esterifying activity. Aging removed unpleasant flavor compounds and helped to stabilize the flavor compounds in mature Daqu. A high-throughput sequencing approach was used to analyze the changing composition of the microbial communities during aging. Aging helped to modify the microbial population to produce better Baijiu by eliminating low-abundance microbial communities and optimizing the proportion of predominant microbial communities. Nine genera of prokaryotic microbes formed the core microbiota in Daqu after aging. Regarding eukaryotic microbes, Zygomycota, the predominant community, increased in the first 2 months, then decreased in the third month of aging, while Ascomycota, the subdominant community, showed the opposite behavior. Absidia, Trichocomaceae_norank and Rhizopus were the predominant genera in the mature Daqu.

Conclusions

Significant correlations between microbiota and physicochemical properties or flavor compounds were observed, indicating that optimizing microbial communities is essential for aging Daqu. This study provides detailed information on aging during Daqu preparation.

Structural and Functional Changes in Prokaryotic Communities in Artificial Pit Mud during Chinese Baijiu Production

Strong-flavor baijiu (SFB) accounts for more than 70% of all Chinese liquor production. In the Chinese baijiu brewing industry, artificial pit mud (APM) has been widely used since the 1960s to construct fermentation cellars for production of high-quality SFB. To gain insights at the systems level into the mechanisms driving APM prokaryotic taxonomic and functional dynamics and into how this variation is connected with high-quality SFB production, we performed the first combined metagenomic, metaproteomic, and metabolomic analyses of this brewing microecosystem. Together, the multi-omics approach enabled us to develop a more complete picture of the changing metabolic processes occurring in APM microbial communities during high-quality SFB production, which will be helpful for further optimization of APM culture technique and improvement of SFB quality.

The Chinese alcoholic beverage strong-flavor baijiu (SFB) gets its characteristic flavor during fermentation in cellars lined with pit mud. Microbes in the pit mud produce key precursors of flavor esters. The maturation time of natural pit mud of over 20 years has promoted attempts to produce artificial pit mud (APM) with a shorter maturation time. However, knowledge about the molecular basis of APM microbial dynamics and associated functional variation during SFB brewing is limited, and the role of this variability in high-quality SFB production remains poorly understood. We studied APM maturation in new cellars until the fourth brewing batch using 16S rRNA gene amplicon sequencing, quantitative PCR, metaproteomics, and metabolomics techniques. A total of 36 prokaryotic classes and 195 genera were detected. Bacilli and Clostridia dominated consistently, and the relative abundance of Bacilli decreased along with the APM maturation. Even though both amplicon sequencing and quantitative PCR showed increased abundance of Clostridia, the levels of most of the Clostridium proteins were similar in both the first- and fourth-batch APM samples. Six genera correlated with eight or more major flavor compounds in SFB samples. Functional prediction suggested that the prokaryotic communities in the fourth-batch APM samples were actively engaged in organic acid metabolism, and the detected higher concentrations of proteins and metabolites in the corresponding metabolic pathways supported the prediction. This multi-omics approach captured changes in the abundances of specific microbial species, proteins, and metabolites during APM maturation, which are of great significance for the optimization of APM culture technique.

IMPORTANCE Strong-flavor baijiu (SFB) accounts for more than 70% of all Chinese liquor production. In the Chinese baijiu brewing industry, artificial pit mud (APM) has been widely used since the 1960s to construct fermentation cellars for production of high-quality SFB. To gain insights at the systems level into the mechanisms driving APM prokaryotic taxonomic and functional dynamics and into how this variation is connected with high-quality SFB production, we performed the first combined metagenomic, metaproteomic, and metabolomic analyses of this brewing microecosystem. Together, the multi-omics approach enabled us to develop a more complete picture of the changing metabolic processes occurring in APM microbial communities during high-quality SFB production, which will be helpful for further optimization of APM culture technique and improvement of SFB quality.

Prokaryotic communities in multidimensional bottom-pit-mud from old and young pits used for the production of Chinese Strong-Flavor Baijiu

The pit mud (PM) prokaryotic communities with obvious difference between old and young PM is essential for solid-fermentation of Chinese Strong-Flavor Baijiu. The bottom-PM (BPM) is considered more important. In this study, the multidimensional prokaryotic communities of old and young BPMs were investigated. The old BPM presented stratified difference within the depth of 0-7 cm, especially, the surface 0-1 cm was characteristic of dominant Caproiciproducens (34.79%). The young BPM showed significant difference between quarter/center and deep corner (1-7 cm), the former were characteristic of abundant Lactobacillus (12.80%-42.72%), while the deep corner was distinctive of dominant Caproiciproducens (17.85%-64.45%). The lactic acid, pH and soluble Ca²⁺ were considered as the 3 most significant environmental factors through redundancy analysis (RDA). This study may help illuminate the BPM aging process, and allow the future artificial regulation of young BPM.

Effects of fortification of Daqu with various yeasts on microbial community structure and flavor metabolism

Fortification of Daqu with isolated functional strains can influence the metabolic activity of the microbial community, and thus alter the flavors of the Baijiu produced with Daqu as a fermentation starter. Here, we analyzed the microbial community dynamics of, and volatile compound production by, Daqu fortified respectively with three high-yield ethyl caproate-producing yeasts (Saccharomyces cerevisiae Y7#09, Hyphopichia burtonii F12507 and Clavispora lusitaniae YX3307), or with a mixture of these three strains, during the fermentation of Baijiu. The microbial community was investigated using Illumina HiSeq technology. Three bacterial genera (Bacillus, Lactobacillus and Enterobacter) and four fungal genera (Pichia, Clavispora, Saccharomyces and Saccharomycopsis) were dominant in the microbial communities. The volatile compounds were examined by gas chromatography-mass spectrometry. Forty-one flavor compounds were detected in all samples, including seven alcohols, 26 esters and four aldehydes. In particular, an increase in ethyl caproate content was associated with Daqu fortified with S. cerevisiae Y7#09, C. lusitaniae YX3307, or the mixed inoculum. The ester content of these fortified Daqu was higher in the later stage of the fermentation than that in unfortified Daqu, or in Daqu fortified with H. burtonii F12507. Our results show that fortification of Daqu with aroma-producing yeast strains influenced the microbial community composition in the Daqu and affected its metabolic activity. Overall, this study reveals the features of fortified Daqu microbial communities in different phases and improves understanding of the relationships between aroma-producing yeast and the metabolic activity of microbial communities in Baijiu production.

Characterization of the microbiota in long- and short-term natural indigo fermentation

The duration for which the indigo-reducing state maintenance in indigo natural fermentation in batch dependent. The microbiota was analyzed in two batches of sukumo fermentation fluids that lasted for different durations (Batch 1: less than 2 months; Batch 2: nearly 1 year) to understand the mechanisms underlying the sustainability and deterioration of this natural fermentation process. The transformation of the microbiota suggested that the deterioration of the fermentation fluid is associated with the relative abundance of Alcaligenaceae. Principal coordinates analysis (PCoA) showed that the microbial community maintained a very stable state in only the long-term Batch 2. Therefore, entry of the microbiota into a stable state under alkaline anaerobic condition is an important factor for maintenance of indigo fermentation for long duration. This is the first report on the total transformation of the microbiota for investigation of long-term maintenance mechanisms and to address the problem of deterioration in indigo fermentation.

Bioturbation effect of fortified Daqu on microbial community and flavor metabolite in Chinese strong-flavor liquor brewing microecosystem

Traditional spontaneous fermentation in microecosystem with microbial successions and environmental variables results in inconsistent quality of fermented foods. We therefore propose the directional bioturbation for microbiota regulation and metabolites production in food fermentation. Here, we revealed the bioturbation effect of fortified Daqu on microbial community based on taxonomic composition, co-occurrence network, and metabolic potential, using Chinese strong-flavor liquor fermentation as a microecosystem. According to principal coordinate analysis, microbial communities were obviously influenced by the bioturbation of fortified Daqu. More specifically, bioturbation increased the abundances of Caproiciproducens, Clostridium, Aspergillus, Candida, Methanobacterium, and Methanosarcina, while decreased that of Lactobacillus. Meanwhile, higher abundances of most genes that encoding enzymes involved in interspecies hydrogen transfer between hexanoic acid bacteria and methanogens were observed in the bioturbated ecosystem by PICRUSt approach. Additionally, co-occurrence analysis showed that bioturbation increased the diversity and complexity of interspecies interactions in microecosystem, which contributed to higher production of flavor metabolites such as hexanoic acid, ethyl hexanoate, and hexyl hexanoate. These results indicated that the bioturbation of fortified Daqu is feasible for flavor metabolism by interspecies interactions of functional microbiota in liquor fermentation. Taken together, it is of great importance for regulating Chinese liquor and even other foods fermentation by bioturbation.

Modeling and Regulation of Higher Alcohol Production through the Combined Effects of the C/N Ratio and Microbial Interaction

Too large of a higher alcohol content has negative effects on the liquor taste and health. Revealing the key microbes and their key driving forces is essential to regulate the higher alcohol content in spontaneous liquor fermentation. Herein, we used high-throughput sequencing associated with a multivariate statistical algorithm to reveal the contributing microbes for higher alcohol production in Chinese light-aroma-type liquor and identified that Saccharomyces and Pichia were the main contributors. In addition, the C/N ratio and microbial interaction were found to significantly affect the production of higher alcohols. Herein, we used response surface methodology to establish a predictive model for higher alcohol production with the regulating factors, and the content of total higher alcohols decreased significantly from 328.80 ± 24.83 to 114.88 ± 5.02 mg/L with the optimized levels of the regulators. This work would facilitate the control of flavor production via regulating microbial communities in food fermentation.

Zooming in on Butyrate-Producing Clostridial Consortia in the Fermented Grains of Baijiu via Gene Sequence-Guided Microbial Isolation

Butyrate, one of the key aroma compounds in Luzhou-flavor baijiu, is synthesized through two alternative pathways: butyrate kinase (buk) and butyryl-CoA: acetate CoA-transferase (but). A lack of knowledge of butyrate-producing microorganisms hinders our ability to understand the flavor formation mechanism of baijiu. Here, temporal dynamics of microbial metabolic profiling in fermented grains (FG) was explored via PICRUSt based on 16S rRNA gene sequences. We found Bacilli and Bacteroidia were the major potential butyrate producers in buk pathway at the beginning of fermentation, while later Clostridia dominated the two pathways. Clone library analysis also revealed that Clostridia (~73% OTUs) was predominant in buk pathway throughout fermentation, followed by Bacilli and Bacteroidia, and but pathway was merely possessed by Clostridia. Afterward, Clostridia-specific 16S rRNA gene sequencing demonstrated Clostridium might be the major butyrate-producing genus in two pathways, which was subsequently evaluated using culture approach. Seventeen Clostridium species were isolated from FG based on 16S rRNA gene sequence-guided medium prediction method. Profiles of short-chain fatty acids and but and buk genes in these species demonstrated phylogenetic and functional diversities of butyrate-producing Clostridium in FG. These findings add to illustrate the diversity of potential butyrate producers during brewing and provide a workflow for targeting functional microbes in complex microbial community.

Construction of Synthetic Microbiota for Reproducible Flavor Compound Metabolism in Chinese Light-Aroma-Type Liquor Produced by Solid-State Fermentation

Natural microbiota plays an essential role in flavor compounds used in traditional food fermentation; however, the fluctuation in natural microbiota results in inconsistency in food quality. Thus, it is critical to reveal the core microbiota for flavor compound production and to construct a synthetic core microbiota for use in constant food fermentation. Here, we reveal the core microbiota based on their flavor production and cooccurrence performance, using Chinese light-aroma-type liquor as a model system. Five genera, Lactobacillus, Saccharomyces, Pichia, Geotrichum, and Candida, were identified to be the core microbiota. The synthetic core microbiota of these five genera presented a reproducible dynamic profile similar to that in the natural microbiota. A Monte Carlo test showed that the effects of five environmental factors (lactic acid, ethanol, and acetic acid contents, moisture, and pH) on the synthetic microbiota distribution were highly significant (P < 0.01), similar to those effects on a natural fermentation system. In addition, 77.27% of the flavor compounds produced by the synthetic core microbiota showed a similar dynamic profile (ρ > 0) with that in the natural liquor fermentation process, and the flavor profile presented a similar composition. It indicated that the synthetic core microbiota is efficient for reproducible flavor metabolism. This work established a method for identifying core microbiota and constructing a synthetic microbiota for reproducible flavor compounds. This work is of great significance for the tractable and constant production of various fermented foods.IMPORTANCE The transformation from natural fermentation to synthetic fermentation is essential in constructing a constant food fermentation process, which is the premise for stably making high-quality food. According to flavor-producing and cooccurring functions in dominant microbes, we provided a system-level approach to identify the core microbiota in Chinese light-aroma-type liquor fermentation. In addition, we successfully constructed a synthetic core microbiota to simulate the microbial community succession and flavor compound production in the in vitro system. The constructed synthetic core microbiota could not only facilitate a mechanistic understanding of the structure and function of the microbiota but also be beneficial for constructing a tractable and reproducible food fermentation process.

Profiling the Clostridia with butyrate-producing potential in the mud of Chinese liquor fermentation cellar

Butyrate and its derivates pertain to the key aroma contributors of strong-flavour baijiu, a kind of Chinese liquors, that is produced from grains by solid-state multispecies anaerobic fermentation in a mud cellar. Microbes inhabiting in the fermentation pit mud largely determines baijiu's flavour and quality. In order to shed light on the microbial functional groups driving butyrate production in pit mud, clone library analysis was firstly performed and the results demonstrated that Clostridia (relative abundance: 50%) and Bacilli (37%) were major groups possessing butyrate kinase (buk) pathway and Clostridia (98%) dominated butyryl-CoA:acetate CoA-transferase (but) pathway. According to Clostridial specific-16S rRNA gene sequencing analysis, we found the resilience character of Clostridial community in pit mud. Amongst Clostridial groups, 32.0% of the sequences were grouped into Clostridiales incertae sedis, followed by Heliobacteriaceae (18.3%) and Clostridiaceae 1 (8.4%). Moreover, Hydrogenispora, Sedimentibacter and Clostridium were the top three abundant genera. Relative abundance of Hydrogenispora was higher in the late days of fermentation, while Sedimentibacter exhibited higher proportion in the early days. Different from the previous studies using universal bacterial primer sets, Hydrogenispora was first reported as one dominant genus in pit mud. As for the reported potential butyrate producer Clostridium, nineteen species were obtained and ten of them were first isolated from the pit mud. Amongst them, buk was identified in eleven species by PCR analysis, while but was identified in the other seven, indicating the species-specific butyrate synthesis pathways of Clostridium. This study provides a perspective on targeting and isolating specific functional microbes in baijiu microbiota with the gene sequence-based medium prediction method.

Effect of Fortified Daqu on the Microbial Community and Flavor in Chinese Strong-Flavor Liquor Brewing Process

Daqu, an important fermentation starter for the production of Chinese liquor, as used in the current study included traditional Daqu and fortified Daqu inoculated with Bacillus velezensis and Bacillus subtilis. To evaluate the effect of fortified Daqu on strong-flavor liquor production, the differences of microbial communities among three inoculation patterns of fermented grains (FG) were analyzed by the Illumina MiSeq platform. A higher relative abundance of dominant genera including Bacillus, Lactococcus, Aspergillus, and Candida, and lower relative abundance of Lactobacillus, were observed in FG50, in which mixed Daqu (traditional: fortified Daqu = 1: 1, w/w, 50% fortified Daqu) was used as the starter. Then, volatile compounds of their distillations were also examined by HS-SPME-GC-MS. The results showed that the contents of skeleton flavor components, mainly including important esters and aromatic compounds, were higher in the corresponding liquor L50, which distillated from FG50. Moreover, most esters mainly positively correlated with Lactobacillus and Candida in the bottom layer of FG fermented with 50% fortified Daqu (FG50-B). Aromatic compounds were strongly positively correlated with Bacillus and Aspergillus in the middle layer of FG with 50% fortified Daqu used (FG50-M). In particular, hexyl hexanoate showed a positive correlation with higher abundances of Ruminococcus in the FG with addition of 100% fortified Daqu (FG100). This study observed microbial compositions in the FG with fortified Daqu addition, and it further revealed the correlations between pivotal microbes and main flavor compounds. These results may help to develop effective strategies to regulate microbes for the brewing process and further improve the flavors of Chinese liquor.

Omics in traditional vegetable fermented foods and beverages

For a long time, food microbiota has been studied using traditional microbiological techniques. With the arrival of molecular or culture-independent techniques, a strong understanding of microbiota dynamics has been achieved. However, analyzing the functional role of microbial communities is not an easy task. The application of omics sciences to the study of fermented foods would provide the metabolic and functional understanding of the microbial communities and their impact on the fermented product, including the molecules that define its aroma and flavor, as well as its nutritional properties. Until now, most omics studies have focused on commercial fermented products, such as cheese, wine, bread and beer, but traditional fermented foods have been neglected. Therefore, the information that allows to relate the present microbiota in the food and its properties remains limited. In this review, reports on the applications of omics in the study of traditional fermented foods and beverages are reviewed to propose new ways to analyze the fermentation phenomena.

Microbiota and Metabolite Profiling of Spoiled Spanish-Style Green Table Olives

The aim of the present study was to assess the malodorous spoilages of Spanish-style green table olives through microbial and metabolite composition using current measuring techniques (e.g., high-throughput DNA sequencing, headspace solid-phase microextraction combined with gas chromatography-mass spectrometry). Under different alkaline and washing conditions, the spoilage fermentations were reproduced with Gordal and Manzanilla olive cultivars using a low salt concentration (71 g L⁻¹ NaCl) in the initial brine. The degradation of lactic acid and significant increases in volatile fatty acids and phenols were found in all the spoiled samples in comparison with the unspoiled control samples. According to high-throughput DNA sequencing, Cardiobacteriaceae and Ruminococcus were the dominant bacteria in the spoiled samples. PLS regression and Pearson’s correlation coefficient analyses revealed positive and negative correlations among microbial communities, metabolites, and sensory spoilage descriptors. Notably, the “zapatera” descriptor was significantly associated with Propionibacterium, which was positively correlated with acetic acid, propionic acid, succinic acid, and methyl propanoate; while the “butyric” descriptor exhibited a significant positive relationship with the genus Ruminococcus, which gave an almost significant correlation with propionic and butyric acids.

Specific Volumetric Weight-Driven Shift in Microbiota Compositions With Saccharifying Activity Change in Starter for Chinese Baijiu Fermentation

Chinese starter Jiuqu, traditionally produced by spontaneous fermentation and always squeezed into bricks, serves as a vital saccharifying agent for simultaneous saccharification and fermentation of Chinese Baijiu. It is important to reveal the key saccharifying microbiota and the driving force to improve the quality of Jiuqu. Here we studied the compositions of the microbiota by high-throughput amplicons sequencing analysis in Jiuqu, and revealed eight bacterial and seven fungal genera as the dominant community members. Among them, Lactobacillus, Aspergillus, Pichia, Saccharomyces, Rhizopus were the main contributors of proteins by metaproteomics analysis. Whereas, only Lactobacillus, Pichia, Rhizopus appeared as key actors for saccharification by secreting three glycosidases and two glycosyltransferases, and it indicated they were the key saccharifying microbiota in Jiuqu. Especially, Rhizopus secreted the most abundant glucoamylase. Interestingly, these three active genera significantly decreased and the key saccharifying enzymes were down-expressed, when Jiuqu was produced in diffused shape with a low volumetric weight. Rhizopus microsporus, the main producer of glucoamylase, was positively correlated with volumetric weight of Jiuqu. It indicated volumetric weight was the major driving force of the key saccharifying microbiota in Jiuqu. This work provides deep insights of key saccharifying microbiota, and indicates the main driving force for the key microbe. Furthermore, this finding can contribute to the improvement of saccharifying agent for food fermentation.

Roles of aging in the production of light-flavored Daqu

Daqu, a complex starting material used for Baijiu production, contains microorganisms, enzymes, and volatile compounds. An important part of Daqu production is aging, but the physicochemical and microbial changes during aging remain largely unknown. This study characterized aging according to physicochemical parameters, volatile compounds, and microbial communities. Aging was found to aid in the stabilization of the physicochemical parameters. Solid-phase microextraction-gas chromatography-mass spectrometry was used to detect 72 types of volatile compounds, which were predominantly alcohols, esters, aldehydes, alkenes, and alkanes. During aging, these compounds changed considerably, but their structures eventually stabilized. A high-throughput sequencing approach was used to analyze the changing composition of the microbial communities. In general, aging helped to enrich and stabilize the microbial population for making Baijiu. A total of 35 bacteria were detected as prokaryotic; among these, 15 had a diversity abundance ratio of more than 1%. The dominant bacteria were from the genus Pantoea, but these decreased with aging, while bacteria from Lactobacillus and Weissella increased. After aging for 2 months, Pantoea, Lactobacillus and Weissella accounted for 0.4%, 54.0%, and 18.9%, respectively. A total of 12 eukaryotic yeast and fungi were detected, the most abundant of which were Incertae_Sedis_incertae_sedis, Saccharomycopsis, Trichocomaceae_unclassified, Pichia, Tremellales_unclassified, and Galactomyces. During aging, the levels of Trichocomaceae_unclassified, Saccharomycopsis, and Galactomyces initially decreased but then increased. Pichia stayed unchanged as aging progressed. In conclusion, aging led to rebalanced interactions among Daqu microbes and was important in improving Daqu quality and ensuring its stability.

Diversity, Function, and Application of Clostridium in Chinese Strong Flavor Baijiu Ecosystem: A Review

Baijiu is a Chinese traditional distilled liquor with an annual yield over 13.12 million tons. Strong flavor baijiu (SFB) also called Luzhou-flavor liquor, takes account for > 70% of the total baijiu produced. SFB is produced by an open solid fermentation process with a complex microbial ecosystem. Clostridium is one of the most important microorganisms for the formation of the main flavor compounds of SFB, such as ethyl caproate. In this paper, we review current research progress on the Clostridium in the SFB ecosystem, focusing on the species diversity, physiological and metabolic features along with interspecies interactions. Systems biology approaches for the study of Clostridium from SFB ecosystems were discussed and explored. Furthermore, current applications of Clostridium in SFB production were discussed.

PRACTICAL APPLICATION

Strong flavor baijiu (SFB) accounts for more than 70% of total yield of Chinese baijiu, which exists for hundreds of years. Clostridium is common in SFB ecosystem and identified to be one of main contributors of flavor compounds in SFB. Study on the Clostridium from SFB ecosystem is not only helpful for the understanding of flavor compounds formation mechanism, but also the improvement of SFB quality. This study focuses on the current researches on the Clostridium species in SFB ecosystem, including the species diversity, physiological and metabolic features, and applications.

Diversity and Function of Microbial Community in Chinese Strong-Flavor Baijiu Ecosystem: A Review

Strong flavor baijiu (SFB), also called Luzhou-flavor liquor, is the most popular Chinese baijiu. It is manufactured via solid fermentation, with daqu as the starter. Microbial diversity of the SFB ecosystem and the synergistic effects of the enzymes and compounds produced by them are responsible for the special flavor and mouthfeel of SFB. The present review covers research studies focused on microbial community analysis of the SFB ecosystem, including the culturable microorganisms, their metabolic functions, microbial community diversity and their interactions. The review specifically emphasizes on the most recently conducted culture-independent analysis of SFB microbial community diversity. Furthermore, the possible application of systems biology approaches for elucidating the molecular mechanisms of SFB production were also reviewed and prospected.

Directly mining a fungal thermostable α-amylase from Chinese Nong-flavor liquor starter

BACKGROUND

Chinese Nong-flavor (NF) liquor is continuously and stably produced by solid-state fermentation technology for 1000 years, resulting in enrichment of special microbial community and enzymes system in its starter. Based on traditional culture-dependent methods, these functional enzymes are hardly obtained. According to our previous metatranscriptomic analysis, which identifies plenty of thermostable carbohydrate-active enzymes in NF liquor starter, the aim of this study is to provide a direct and efficient way to mine these thermostable enzymes.

RESULTS

In present study, an alpha-amylase (NFAmy13A) gene, which showed the highest expression level of enzymes in starch degradation at high temperature stage (62 °C), was directly obtained by functional metatranscriptomics from Chinese Nong-flavor liquor starter and expressed in Pichia pastoris. NFAmy13A had a typical signal peptide and shared the highest sequence identity of 64% with α-amylase from Aspergillus niger. The recombinant enzyme of NFAmy13A showed an optimal pH at 5.0-5.5 and optimal temperature at 60 °C. NFAmy13A was activated and stabilized by Ca²⁺, and its half-lives at 60 and 70 °C were improved significantly from 1.5 and 0.4 h to 16 and 0.7 h, respectively, in the presence of 10 mM CaCl₂. Meanwhile, Hg²⁺, Co²⁺ and SDS largely inhibited its activity. NFAmy13A showed the maximum activity on amylopectin, followed by various starches, amylose, glycogen, and pullulan, and its specificity activity on amylopectin was 200.4 U/mg. Moreover, this α-amylase efficiently hydrolyzed starches (from corn, wheat, and potato) at high concentrations up to 15 mg/ml.

CONCLUSIONS

This study provides a direct way to mine active enzymes from man-made environment of NF liquor starter, by which a fungal thermostable α-amylase (NFAmy13A) is successfully obtained. The good characteristics of NFAmy13A in degrading starch at high temperature are consistent with its pivotal role in solid-state fermentation of NF liquor brewing. This work would stimulate mining more enzymes from NF liquor starter and studying their potentially synergistic roles in NF liquor brewing, thus paving the way toward the optimization of liquor production and improvement of liquor quality in future.

Environmental Microbiota Drives Microbial Succession and Metabolic Profiles during Chinese Liquor Fermentation

Many microorganisms in the environment participate in the fermentation process of Chinese liquor. However, it is unknown to what extent the environmental microbiota influences fermentation. In this study, high-throughput sequencing combined with multiphasic metabolite target analysis was applied to study the microbial succession and metabolism changes during Chinese liquor fermentation from two environments (old and new workshops). SourceTracker was applied to evaluate the contribution of environmental microbiota to fermentation. Results showed that Daqu contributed 9.10 to 27.39% of bacterial communities and 61.06 to 80.00% of fungal communities to fermentation, whereas environments (outdoor ground, indoor ground, tools, and other unknown environments) contributed 62.61 to 90.90% of bacterial communities and 20.00 to 38.94% of fungal communities to fermentation. In the old workshop, six bacterial genera (Lactobacillus [11.73% average relative abundance], Bacillus [20.78%], Pseudomonas [6.13%], Kroppenstedtia [10.99%], Weissella [16.64%], and Pantoea [3.40%]) and five fungal genera (Pichia [55.10%], Candida [1.47%], Aspergillus [10.66%], Saccharomycopsis [22.11%], and Wickerhamomyces [3.35%]) were abundant at the beginning of fermentation. However, in the new workshop, the change of environmental microbiota decreased the abundances of Bacillus (5.74%), Weissella (6.64%), Pichia (33.91%), Aspergillus (7.08%), and Wickerhamomyces (0.12%), and increased the abundances of Pseudomonas (17.04%), Kroppenstedtia (13.31%), Pantoea (11.41%), Acinetobacter (3.02%), Candida (16.47%), and Kazachstania (1.31%). Meanwhile, in the new workshop, the changes of microbial community resulted in the increase of acetic acid, lactic acid, malic acid, and ethyl acetate, and the decrease of ethyl lactate during fermentation. This study showed that the environmental microbiota was an important source of fermentation microbiota and could drive both microbial succession and metabolic profiles during liquor fermentation.IMPORTANCE Traditional solid-state fermentation of foods and beverages is mainly carried out by complex microbial communities from raw materials, starters, and the processing environments. However, it is still unclear how the environmental microbiota influences the quality of fermented foods and beverages, especially for Chinese liquors. In this study, we utilized high-throughput sequencing, microbial source tracking, and multiphasic metabolite target analysis to analyze the origins of microbiota and the metabolic profiles during liquor fermentation. This study contributes to a deeper understanding of the role of environmental microbiota during fermentation.

Biochemical characterisation and dominance of different hydrolases in different types of Daqu - a Chinese industrial fermentation starter

BACKGROUND

Daqu is a fermentative saccharification agent that is used to initiate fermentation in the production of Chinese liquor and vinegar. This study investigated the differences of amylase, protease and esterase in dominance of different types of Daqu, which can be useful for quality control and flavor improvement of Daqu production by enzyme technology.

RESULTS

Hydrolase activities in different Daqu samples were compared by principal component analysis (PCA). Based on protein electrophoresis and ¹ H NMR spectroscopy, the protein patterns and metabolites in Daqu were further analysed. The results indicated that the highest amylase activities and diversities were found in low/medium-temperature of Daqu which had light-flavour and strong-flavour. Proteases play a significant role in determining the quality of high-temperature Daqu samples which had a sauce-flavour. Furthermore, the contributions of esterase to both strong and sauce flavour development in high-temperature Daqu are similar.

CONCLUSION

Results from the present work showed that differences in amylase, protease and esterase play a leading role in different types of Daqu, which can be useful for quality control and technology development of Daqu. © 2017 Society of Chemical Industry.

Synergistic Effect in Core Microbiota Associated with Sulfur Metabolism in Spontaneous Chinese Liquor Fermentation

Microbial sulfur metabolism plays crucial roles in various food and alcoholic beverage fermentations. 3-(Methylthio)-1-propanol and dimethyl disulfide are important sulfur compounds in fermented foods and alcoholic beverages. Here, we studied the dynamics of these two compounds during spontaneous Chinese liquor fermentation. The two compounds reached the maximum concentration at day 10 and the maximum production rate at day 3. Metatranscriptomic analysis at days 3 and 10 revealed a total of 354 metabolically active microorganisms. Saccharomyces and Lactobacillus were identified as core microbiota critical for sulfur compound production based on both the transcript abundances of the principal genes and the distribution frequencies of 31 enzymes involved in sulfur metabolism. Saccharomyces transcribed genes encoding 23 enzymes related to the generation of 3-(methylthio)-1-propanol and dimethyl disulfide, and Lactobacillus was active in the methyl cycle, which recycles methionine, the precursor of the two sulfur compounds. Furthermore, the sulfur metabolism-related characteristics of two representative species were studied in coculture during a simulated fermentation. Saccharomyces cerevisiae JZ109 produced 158.4 μg/liter 3-(methylthio)-1-propanol and 58.5 μg/liter dimethyl disulfide in monoculture, whereas Lactobacillus buchneri JZ-JN-2017 could not produce these two compounds in monoculture. Their coculture significantly enhanced the generation of 3-(methylthio)-1-propanol (350.0 μg/liter) and dimethyl disulfide (123.8 μg/liter). In addition, coculture significantly enhanced the gene transcriptions (fold change, 1.5 to ∼55.0) that convert methionine to these two compounds in S. cerevisiae and in the methyl cycle of L. buchneri This study reveals a novel synergistic effect between members of the core microbiota in the production of sulfur compounds via methionine recycling in spontaneous Chinese liquor fermentation.IMPORTANCE Sulfur compounds play a crucial role in the aroma quality of various fermented foods and alcoholic beverages. However, it is unclear how these compounds are produced by microbes during their spontaneous fermentations. Here, we identified the core microbiota (Saccharomyces and Lactobacillus) associated with sulfur metabolism by determining both transcript abundance and distribution frequency of each genus in spontaneous Chinese liquor fermentation. This study provides a system-level analysis of sulfur metabolism by the metatranscriptomic analysis and culture-dependent methods. It sheds new light on how the metabolic behavior of the microbiota contributes to the liquor aroma quality. Furthermore, this work reveals a novel synergistic effect between Saccharomyces and Lactobacillus in the production of sulfur compounds, in which Lactobacillus regenerates the precursor methionine for sulfur compound production by Saccharomyces Our findings can contribute to the enhancement of aroma characteristics in Chinese liquor and open new avenues for improving various food and alcoholic beverage fermentation processes.

New microbial resource: microbial diversity, function and dynamics in Chinese liquor starter

Traditional Chinese liquor (Baijiu) solid state fermentation technology has lasted for several thousand years. The microbial communities that enrich in liquor starter are important for fermentation. However, the microbial communities are still under-characterized. In this study, 454 pyrosequencing technology was applied to comprehensively analyze the microbial diversity, function and dynamics of two most-consumed liquor starters (Jiang- and Nong-flavor) during production. In total, 315 and 83 bacterial genera and 72 and 47 fungal genera were identified in Jiang- and Nong-flavor liquor starter, respectively. The relatively high diversity was observed when the temperature increased to 70 and 62 °C for Jiang- and Nong-flavor liquor starter, respectively. Some thermophilic fungi have already been isolated. Microbial communities that might contribute to ethanol fermentation, saccharification and flavor development were identified and shown to be core communities in correlation-based network analysis. The predictively functional profile of bacterial communities showed significant difference in energy, carbohydrate and amino acid metabolism and the degradation of aromatic compounds between the two kinds of liquor starters. Here we report these liquor starters as a new functionally microbial resource, which can be used for discovering thermophilic and aerobic enzymes and for food and feed preservation.

Metatranscriptomics Reveals the Functions and Enzyme Profiles of the Microbial Community in Chinese Nong-Flavor Liquor Starter

Chinese liquor is one of the world's best-known distilled spirits and is the largest spirit category by sales. The unique and traditional solid-state fermentation technology used to produce Chinese liquor has been in continuous use for several thousand years. The diverse and dynamic microbial community in a liquor starter is the main contributor to liquor brewing. However, little is known about the ecological distribution and functional importance of these community members. In this study, metatranscriptomics was used to comprehensively explore the active microbial community members and key transcripts with significant functions in the liquor starter production process. Fungi were found to be the most abundant and active community members. A total of 932 carbohydrate-active enzymes, including highly expressed auxiliary activity family 9 and 10 proteins, were identified at 62°C under aerobic conditions. Some potential thermostable enzymes were identified at 50, 62, and 25°C (mature stage). Increased content and overexpressed key enzymes involved in glycolysis and starch, pyruvate and ethanol metabolism were detected at 50 and 62°C. The key enzymes of the citrate cycle were up-regulated at 62°C, and their abundant derivatives are crucial for flavor generation. Here, the metabolism and functional enzymes of the active microbial communities in NF liquor starter were studied, which could pave the way to initiate improvements in liquor quality and to discover microbes that produce novel enzymes or high-value added products.