PCR-DGGE analysis on microbial communities in pit mud of cellars used for different periods of time

Assembly mechanisms and function features of prokaryotic communities in artificial pit mud related to soil type and inoculum

The prokaryotic community of artificial pit mud (APM), which is manufactured using fresh soil as the raw material, pit mud (PM) as the inoculum, and yellow water (YW) as the nutrient source, significantly affect the quality of strong-flavor Baijiu. Here, the APM assembly mechanisms and function features under the different treatments were explored by microcosmic experiments. The results revealed that the soil type could directly influence the APM physicochemical properties, and the inoculum mainly affected the typical organic acids. Microbial analyses revealed that the influence of soil type (22.69 %) and inoculum (20.60 %) on the APM prokaryotic community was greater than that of YW nutrient (7.50 %). Among them, black soil was more conducive to the stability, compactness, and modularization tendency of the co-occurrence network, compared to loess soil. Assembly model showed that most APMs predominantly relied on the stochastic process (|βNTI| ≤ 2), and black soil might facilitate the balance of the stochastic and deterministic processes. Metabolism annotation unveiled that new PM inoculum stimulated lipopolysaccharide biosynthesis, sphingolipid metabolism and lysosome, affecting the stability of APM individual microorganism compared to old PM inoculum. The environmental adaptation revealed that old PM inoculum, black soil, and YW nutrient contributed to the broader environmental thresholds, enhancing the APM adaptability to diverse feedstock environments. These findings could provide valuable insights into standardizing APM in the future.

Structure and metabolic function of spatiotemporal pit mud microbiome

BACKGROUND

Pit mud (PM) hosts diverse microbial communities, which serve as a medium to impart flavor and quality to Baijiu and exhibit long-term tolerance to ethanol and acids, resulting in a unique ecosystem. However, the ecology and metabolic functions of PM remain poorly understood, as many taxa in PM represent largely novel lineages. In this study, we used a combination of metagenomic analysis and chemical derivatization LC-MS analysis to provide a comprehensive overview of microbial community structure, metabolic function, phylogeny, horizontal gene transfer, and the relationship with carboxyl compounds in spatiotemporal PM samples.

RESULTS

Our findings revealed three distinct stages in the spatiotemporal changes of prokaryotic communities in PM: an initial phase dominated by Lactobacillus, a transitional phase, and a final state of equilibrium. Significant variations in α- and β-diversity were observed across different spatial and temporal PM samples. We identified 178 medium- and high-quality non-redundant metagenome-assembled genomes (MAGs), and constructed their phylogenetic tree, depicting their roles in the carbon, nitrogen, and sulfur cycles. The Wood-Ljungdahl pathway and reverse TCA cycle were identified as the main carbon fixation mechanisms, with both hydrogenotrophic and aceticlastic methanogens playing a major role in methane production, and methylotrophic pathway observed in older PM. Furthermore, we identified relationships between prokaryotes and 29 carboxyl metabolites, including medium- and long-chain fatty acids. Horizontal gene transfer (HGT) was widespread in PM, particularly among clostridia, Bacteroidota, Bacilli, and Euryarchaeota, and was shown to play critical roles in fermentation dynamics, carbon fixation, methane production, and nitrogen and sulfur metabolism.

CONCLUSION

Our study provides new insights into the evolution and function of spatiotemporal PM, as well as its interactions with carboxyl metabolites. Lactobacillus dominated in new PM, while methanogens and clostridia were predominant in older or deeper PM layers. The three distinct stages of prokaryotic community development in PM and HGT played critical roles in metabolic function of spatiotemporal PM. Furthermore, this study highlights the importance of α-diversity, β-diversity, methanogens, and Clostridium as useful indicators for assessing PM quality in the production of high-quality Baijiu.

Bacterial diversity associated with volatile compound accumulation in pit mud of Chinese strong-flavor baijiu pit

Pit mud quality is a key parameter that impacts the quality of Chinese strong-flavor Baijiu production.This study was developed to explore spatial bacterial community distributions and the relationships between these distributions and the volatile compound accumulation within the pit mud used in the production of Chinese strong-flavor Baijiu. The results revealed Lactobacillus pasteurii and Limnochorda pilosa were found to be the dominant bacteria present in the upper wall, middle wall, and bottom pit mud layers, whereas the Clostridium genus was detectable at high levels in the lower layer of the pit wall and played a role in contributing to the overall aroma and flavor compounds in produced Chinese strong-flavor Baijiu, with Clostridium abundance being strongly correlated with caproic acid, ethyl caproate, ethyl butyrate, and hexanol levels as well as moderately correlated with butyric acid levels. The abundance of the Lactobacillus genus was positively correlated with levels of ethyl lactate, 1-butanol, and 2,3-butanediol. Limnochorda pilosa was closely associated with ethyl acetate levels. Additionally, the correlations between bacterial communities and chemical properties also investigated, and the results demonstrated PO4^3-, total carbon, K⁺, humus, NH₄⁺-N, and Mg²⁺ levels significantly affected the bacterial community structure of pit mud, and they were positively correlated with the relative abundance of Clostridium. Together, these findings can serve as a foundation for future studies exploring the mechanisms whereby volatile compounds accumulate in different pit mud layers, which facilitates the fermentation regulation and pit mud quality improvement of Chinese strong-flavor Baijiu.

Microbial community spatial structures in Luzhou-flavored liquor pit muds with different brewing materials

Background

Although studies have shown that Bacteroidetes, Clostridiales, and Lactobacillales are the main components of the microbial community in pit mud during the brewing of Luzhou-flavored liquor, little is known about the effect of brewing materials on spatial structures of this microbiome.

Methods

High-throughput sequencing of the V4-V5 region of prokaryotic 16S rRNA gene was performed to analyze the microbial community diversity and spatial heterogeneity in Luzhou-flavored liquor pit muds with different brewing ingredients. The structural characteristics and heterogeneous spatial distribution of the pit mud microbial communities were examined using bioinformatics and multivariate statistical analysis methods.

Results

Our results showed that Euryarchaeota, Actinobacteria, Bacteroidetes, Chlorobi, Chloroflexi, Firmicutes, Proteobacteria, Synergistetes, Tenericutes, and WWE1 were the dominant phyla in the pit mud microbiome. The Shannon and Simpson indices of the pit mud microbiome with three grains (M3G) in the upper layer were significantly lower than those in middle layer and bottom, whereas those of the pit mud microbiome with five grains (M5G) in bottom were significantly lower than those in middle layer (p < 0.05). There were significant differences in the microbial community compositions between the pit muds with different brewing ingredients and locations in the same pit (p < 0.05). T78 of Anaerolinaceae, Butyrivibrio, Dehalobacter_Syntrophobotulus, Desulfosporosinus, Asteroleplasma, and vadinCA02 of Synergistaceae were significantly enriched in M3G, whereas Prevotella, Vagococcus, Caldicoprobacter, Butyrivibrio, Coprococcus, Dorea, Sporanaerobacter, Tepidimicrobium, TissierellaSoehngenia, RFN20 of Erysipelotrichaceae, Sutterella, 125ds10 of Alteromonadales, Vibrio, and Sphaerochaeta were significantly enriched in M5G. This study provides a theoretical basis for exploring the influence of brewing ingredients in pit muds on the production of Luzhou-flavored liquor and the specific influence of pit mud microorganisms in different locations on liquor production.

The Depth-Depended Fungal Diversity and Non-depth-Depended Aroma Profiles of Pit Mud for Strong-Flavor Baijiu

Microorganisms in pit mud are the essential factor determining the style of strong flavor Baijiu. The spatial distribution characteristics of fungal communities and aroma in the pit mud for strong flavor Baijiu from Xinjiang, China, were investigated using Illumina MiSeq high-throughput sequencing and electronic nose technology. A total of 138 fungal genera affiliated with 10 fungal phyla were identified from 27 pit mud samples; of these, Saccharomycopsis, Aspergillus, and Apiotrichum were the core fungal communities, and Aspergillus and Apiotrichum were the hubs that maintain the structural stability of fungal communities in pit mud. The fungal richness and diversity, as well as aroma of pit mud, showed no significant spatial heterogeneity, but divergences in pit mud at different depths were mainly in pH, total acid, and high abundance fungi. Moisture, NH4 +, and lactate were the main physicochemical factors involved in the maintenance of fungal stability and quality in pit mud, whereas pH had only a weak effect on fungi in pit mud. In addition, the fungal communities of pit mud were not significantly associated with the aroma. The results of this study provide a foundation for exploring the functional microorganisms and dissecting the brewing mechanism of strong flavor Baijiu in Xinjiang, and also contributes to the improvement of pit mud quality by bioaugmentation and controlling environmental physicochemical factors.

Characterization of Microbial Diversity and Community Structure in Fermentation Pit Mud of Different Ages for Production of Strong-Aroma Baijiu

In the traditional fermentation process of strong-aroma Baijiu, a fermentation pit mud (FPM) provides many genera of microorganisms for fermentation. However, the functional microorganisms that have an important effect on the quality of Baijiu and their changes with the age of fermentation pit (FP) are poorly understood. Herein, the Roche 454 pyrosequencing technique and a phospholipid fatty-acid analysis were employed to reveal the structure and diversity of prokaryotic communities in FPM samples that have been aged for 5, 30, and 100 years. The results revealed an increase in total prokaryotic biomass with an FP age; however, Shannon’s diversity index decreased significantly (p < 0.01). These results suggested that a unique microbial community structure evolved with uninterrupted use of the FP. The number of functional microorganisms, which could produce the flavor compounds of strong-aroma Baijiu, increased with the FP age. Among them, Clostridium and Ruminococcaceae are microorganisms that directly produce caproic acid. The increase of their relative abundance in the FPM might have improved the quality of strong-aroma Baijiu. Syntrophomonas, Methanobacterium, and Methanocorpusculum might also be beneficial to caproic acid production. They are not directly involved but provide possible environmental factors for caproic acid production. Overall, our study results indicated that an uninterrupted use of the FP shapes the particular microbial community structure in the FPM. This research provides scientific support for the concept that the aged FP yields a high-quality Baijiu.

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.

Gut microbiota composition and frailty in elderly patients with Chronic Kidney Disease

Background

Frailty is common in older patients affected by chronic kidney disease (CKD). Since gut microbiota (gMB) may contribute to frailty, we explored possible associations between gMB and frailty in CKD.

Methods

We studied 64 CKD patients (stage 3b-4), categorized as frail (F, 38) and not frail (NF, 26) according to Fried criteria, and 15 controls (C), all older than 65 years. In CKD we assessed serum C-reactive protein, blood neutrophil/lymphocyte ratio, Malnutrition-inflammation Score (MIS); gMB was studied by denaturing gel gradient electrophoresis (DGGE), high-throughput sequencing (16S r-RNA gene), and quantitative real-time PCR (RT-PCR).

Results

No differences in alpha diversity between CKD and C and between F and NF patients emerged, but high-throughput sequencing showed significantly higher abundance of potentially noxious bacteria (Citrobacter, Coprobacillus, etc) and lower abundance of saccharolytic and butyrate-producing bacteria (Prevotella spp., Faecalibacterium prausnitzii, Roseburia spp.), in CKD respect to C. Mogibacteriaceae family and Oscillospira genus abundance was positively related to inflammatory indices in the whole CKD cohort, while that of Akkermansia, Ruminococcus and Eubacterium genera was negatively related. Compared with NF, in F there was a higher abundance of some bacteria (Mogibacteriacee, Coriobacteriacee, Eggerthella, etc), many of which have been described as more abundant in other diseases.

Conclusions

These results suggest that inflammation and frailty could be associated to gMB modifications in CKD.

Impact of cystic fibrosis disease on archaea and bacteria composition of gut microbiota

Cystic fibrosis is often associated with intestinal inflammation due to several factors, including altered gut microbiota composition. In this study, we analyzed the fecal microbiota among patients with cystic fibrosis of 10–22 years of age, and compared the findings with age-matched healthy subjects. The participating patients included 14 homozygotes and 14 heterozygotes with the delF508 mutation, and 2 heterozygotes presenting non-delF508 mutations. We used PCR-DGGE and qPCR to analyze the presence of bacteria, archaea and sulfate-reducing bacteria. Overall, our findings confirmed disruption of the cystic fibrosis gut microbiota. Principal component analysis of the qPCR data revealed no differences between homozygotes and heterozygotes, while both groups were distinct from healthy subjects who showed higher biodiversity. Archaea were under the detection limit in all homozygotes subjects, whereas methanogens were detected in 62% of both cystic fibrosis heterozygotes and healthy subjects. Our qPCR results revealed a low frequency of sulfate-reducing bacteria in the homozygote (13%) and heterozygote (13%) patients with cystic fibrosis compared with healthy subjects (87.5%). This is a pioneer study showing that patients with cystic fibrosis exhibit significant reduction of H₂-consuming microorganisms, which could increase hydrogen accumulation in the colon and the expulsion of this gas through non-microbial routes.

Analysis of the bacterial community in aged and aging pit mud of Chinese Luzhou-flavour liquor by combined PCR-DGGE and quantitative PCR assay

BACKGROUND

The community structure of bacteria in aged and aging pit mud, which was judged according to their sensory and physicochemical characteristics, was analysed using polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) and quantitative real-time PCR (qPCR).

RESULTS

The phyla Firmicutes, Actinobacteria, Proteobacteria, Synergistetes and Unclassified Bacteria were detected and the fermentative Firmicutes was predominant in both types of pit mud in the PCR-DGGE analysis. Among Firmicutes, Clostridiales was dominant in aged pit mud while Bacillales and Lactobacillales were dominant in aging pit mud. The diversity of bacterial communities in aged pit mud was higher than that in aging pit mud. In the qPCR analysis the abundance of Clostridium IV in aged pit mud was higher than that in aging pit mud and there were significant differences in the quantity of Clostridium IV between aged and aging pit mud of the same cellar (P < 0.05).

CONCLUSION

There were some significant differences in the microbial community structure between aged and aging pit mud. The differences in the quantity of Clostridium IV might be involved in the distinction that the aged pit mud has a strong aroma while the aging pit mud does not.

Proteomic and high-throughput analysis of protein expression and microbial diversity of microbes from 30- and 300-year pit muds of Chinese Luzhou-flavor liquor

Luzhou-flavor liquor is fermented based on the metabolism of special microbial communities in pit. In this study, total proteins and DNAs of microbes from 30- and 300-year pit muds were firstly extracted. Meanwhile, an efficient approach for protein extraction with increased protein content was optimized. iTRAQ-based proteomic was then applied to investigate the aroma-forming functional protein expression of microbes from the samples. Furthermore, high-throughput sequencing of 16S rDNA was employed to reveal microbial diversity. We comparatively identified 63 proteins of aroma-forming functional microbes in these samples, and found that 59 of these proteins were highly expressed in the 300-year pit mud. Those aroma-forming functional proteins were found to be involved in methanogenesis, as well as the formation of caproic acid and butyric acid during the liquor fermentation. High-throughput sequencing revealed that the microbes most commonly found in both samples were members of phylum Firmicutes (by 97% sequence similarity), both of which, along with another common Methanobacterium, were important components of aroma-forming functional colonies in the pit muds for the brewing of Chinese liquor. The findings in this study afford us new insight into the different protein expression levels and microbial communities in two pit muds.