Analysis of Clostridium cluster I community diversity in pit mud used in manufacture of Chinese Luzhou-flavor liquor

Clostridium lapidicellarium sp. nov. and Clostridium moutaii sp. nov., two species isolated from fermentation cellar-producing sauce-flavour Chinese baijiu

Clostridium is an important microbial component in pit mud due to its ability to produce alcohol and short-chain fatty acids. This study presents the characterization and taxonomy of two Gram-stain-positive, strictly anaerobic, rod-shaped mesophilic bacterial strains, designated MT-113T and MT-5T, isolated from pit mud in a fermentation cellar used for producing sauce-flavour Chinese baijiu. Phylogenetic analysis based on genome and 16S rRNA gene sequences of strains MT-113T and MT-5T indicates their affiliation with the genus Clostridium sensu stricto (Cluster I of the Clostridia), with C. luticellarii FW431T and C. aromativorans WLY-B-L2T as the closest related species. The major cellular fatty acids (>10.0%) of both strains are C14 : 0 and summed feature 1 (iso-C15 : 1 h and/or C13 : 0 3-OH). The G+C molar contents of the complete genomes for strains MT-113T and MT-5T are 35.84 and 32.74 mol%, respectively. The average nucleotide identity and average amino acid identity values between strains MT-113T, MT-5T, C. aromativorans WLY-B-L2T and C. luticellarii FW431T range from 79 to 85%. The primary products of glucose fermentation by MT-113T are acetic, butyric and isovaleric acids, while those of MT-5T are acetic, isobutyric, butyric and isovaleric acids. Based on their phenotypic, chemotaxonomic and phylogenetic characteristics, strains MT-113T (=CGMCC 1.18018T = JCM 36532T) and MT-5T (=CGMCC 1.18016T = JCM 36530T) are proposed as the type strains of two novel species of the genus Clostridium, namely Clostridium lapidicellarium sp. nov. and Clostridium moutaii sp. nov., respectively.

Clostridium aromativorans sp. nov., isolated from pit mud used for producing Wuliangye baijiu

A strictly anaerobic, gram-positive bacterium, designated as WLY-B-L2^T, was isolated from pit mud of a fermentation pit located at Wuliangye 501# baijiu workshop in Yibin (Sichuan province, PR China). The strain was strictly anaerobic, Gram-positive with straight or somewhat rod shaped cells which were 0.5-0.7 μm wide and 1.7-3.1 μm long, arranged singly or in pairs. The strain can utilize D-galacturonic acid, methyl pyruvate, L-lactamine, L-alanyl - L-glutamine, L-alanyl - L-histidine, glycerol, pyruvate, L-alanyl - L-threonine, L-methionine, L-phenylalanine, L-valine + L-aspartic acid, L-serine, L-valine, and thymidine as carbon sources. Major cellular fatty acids are C_{16: 0} (24.6%), anteiso-C_{15: 0} (16.5%), and iso-C_{15: 0} (14.1%). Based on 16S rRNA gene sequence, WLY-B-L2^T is most closely related to Clostridium luticellarii FW431^T; they exhibit 97.42% 16S rRNA similarity. Additionally, the digital DNA-DNA hybridization (dDDH) value between them is 28.10%. WLY-B-L2^T has a G + C content of 34.16 mol%. Based on the evidence presented here, WLY-B-L2^T (CICC 25133^T = JCM 35127^T) is proposed as the type strain of a novel species, designated as Clostridium aromativorans sp. nov, that could produce butyric acid and volatile flavor components, such as ethyl valerate, ethyl acetate and 2-pentanone.

Simulated Fermentation of Strong-Flavor Baijiu through Functional Microbial Combination to Realize the Stable Synthesis of Important Flavor Chemicals

The solid-state fermentation of Baijiu is complicated by the co-fermentation of many microorganisms. The instability of the composition and abundance of the microorganisms in the fermentation process leads to fluctuations of product quality, which is one of the bottleneck problems faced by the Strong-flavor Baijiu industry. In this study, we established a combination of functional microorganisms for the stable fermentation of the main flavor compounds of Baijiu, including medium and long-chain fatty acid ethyl esters such as hexanoic acid, ethyl ester; butanoic acid, ethyl ester; octanoic acid, ethyl ester; acetic acid, ethyl ester; 9,12-octadecadienoic acid, ethyl ester; and decanoic acid, ethyl ester in the fermented grains. Our study investigated the effects of microbial combinations on the fermentation from three aspects: microbial composition, microbial interactions, and microbial association with flavor compounds. The results showed that the added functional microorganisms (Lactobacillus, Clostridium, Caproiciproducens, Saccharomyces, and Aspergillus) became the dominant species in the fermentation system and formed positive interactions with other microorganisms, while the negative interactions between microorganisms were significantly reduced in the fermentation systems that contained both Daqu and functional microorganisms. The redundancy analysis showed that the functional microorganisms (Lactobacillus, Saccharomyces, Clostridium, Cloacibacterium, Chaenothecopsis, Anaerosporobacter, and Sporolactobacillus) showed strong positive correlations with the main flavor compounds (hexanoic acid, ethyl ester; lactic acid, ethyl ester; butanoic acid, ethyl ester; acetic acid, ethyl ester; and octanoic acid, ethyl ester). These results indicated that it was feasible to produce Baijiu with a functional microbial combination, and that this could promote stable Baijiu production.

Chemotaxis of Clostridium Strains Isolated from Pit Mud and Its Application in Baijiu Fermentation

Clostridium is the key bacteria that inhabits the pit mud in a fermentation cell, for the production of strong-flavor Baijiu. Its activities in the process of Baijiu fermentation is closely related to the niches of pit mud and cells. After multiple rounds of underground fermentation, Clostridium has been domesticated and adapted to the environment. The mechanisms of clostridia succession in the pit mud and how they metabolize nutrients present in grains are not clear. In this study, 15 Clostridium species including three firstly reported ones (Clostridium tertium, Clostridium pabulibutyricum and Clostridium intestinale) in strong-flavor Baijiu pit mud, were isolated from the pit mud. Eighty one percent of these Clostridium strains are motile, and most of them show chemotaxis to organic acids, glutathione, saccharides and lactic acid bacteria. In a simulated Baijiu fermentation system, Clostridium migrated from pit mud to fermented grains with the addition of chemokine lactic acid, resulting in the production of acetic acid and butyric acid. The results help to understand the succession mechanism of Clostridium in pit mud, and provide a reference for regulation of lactic acid level in fermented grains during Baijiu fermentation.

Fungal Diversity Profiles in Pit Mud Samples from Chinese Strong-Flavour Liquor Pit

Pit mud, a specific fermented soil, is an essential material for the fermentation of Chinese strong-flavour liquor. However, few studies to date have sought to characterize the spatial profiles of pit mud fungal communities in fermentation cellars from Chinese strong-flavour liquor distilleries. In this analysis, differences in fungal community structures and physicochemical properties in pit mud samples from different spatial positions within fermentation cellars were analyzed, revealing unique characteristic multidimensional pit mud fungal community profiles. Penicillium roqueforti, Pichia kudriavzevii, Aotearoamyces nothofagi, Penicillium robsamsonii, Alternaria arborescens, Trichosporon insectorum, Seltsamia ulmi, Trichosporon coremiiforme, Malassezia restricta were dominant in the pit mud samples form the upper cellar wall, whereas Metarhizium frigidum, Calonectria pseudoreteaudii, Penicillium clavigerum, Fusarium equiseti, Simplicillium chinense, Aspergillus intermedius, Trichosporon coremiiforme, Fusarium circinatum, Alternaria radicina, Aspergillus heterocaryoticus were predominant in the middle cellar wall. Alternaria radicina, Cladosporium chasmanthicola, Alternaria helianthiinficiens, Penicillium argentinense, Antarctomyces psychrotrophicus, and Trichosporon inkin are majorly present in the down cellar wall layer. Bipolaris axonopicola, Ramgea ozimecii, Penicillium argentinense, Calonectria queenslandica, Metarhizium robertsii, and Penicillium roqueforti were identified as the dominant fungi in pit mud samples from the cellar bottom. Additionally, Alternaria destruens and Alternaria doliconidium are present at notably high levels in all layers of pit mud samples. Moisture, pH, PO₄^3-, acetic acid, humus, K⁺, Mg²⁺, Ca²⁺, butyric acid, and caproic acid levels in these different pit mud positions exhibited a rising incremental pattern from the upper wall layer to the bottom layer, whereas lactic acid levels were significantly lower in the bottom pit mud layer relative to these other layers. Moisture, pH, and NH₄⁺-N were identified as the three most significant factors associated with fungal community composition through a redundancy analysis. Overall, these findings may offer a theoretical foundation for future efforts to improve or standardize artificial pit mud.

Occurrence, Diversity, and Character of Bacillaceae in the Solid Fermentation Process of Strong Aromatic Liquors

Strong aromatic liquors, also known as strong aromatic Baijiu (SAB) in China, are manufactured by solid fermentation, with a multi-microbe mixing and cooperative fermentation process that uses Daqu as a brewing starter. Bacillaceae have a specific action in food fermentation, such as soybean and wine, and more recent studies have found Bacillaceae play important roles in the SAB making industry. This review describes the diversity, functionality, and influence of Bacillaceae in Daqu, pit mud, Zaopei, Huangshui within making processes of SAB. Furthermore, aromatic flavor components from the Bacillaceae metabolism of SAB are discussed in this review. Ultimately, the resulting improvements and deeper understanding will benefit practical efforts to apply representatives of Bacillaceae in improving the quality of SAB as well as biological control of the micro-ecological environment of brewing.

Flavor mystery of Chinese traditional fermented baijiu: The great contribution of ester compounds

Chinese traditional fermented baijiu is a famous alcoholic beverage with unique flavor. Despite its consumption for millennia, the flavor mystery behind baijiu is still unclear. Studies indicate that esters are the most important flavor substances, and bring health benefits. However, the aroma contribution and formation mechanism of esters still need to be clarified to reveal the flavor profile of baijiu. This review systematically summarizes all the 510 esters and finds 9 ethyl esters contribute greatly to the flavor of baijiu. The 508 different microbial species that have been identified affect the synthesis of esters through fatty acid and amino acid metabolism. The determination of minimum functional microbial groups and the analysis of their metabolic characteristics are crucial to reveal the mechanism of formation of baijiu flavor, and ensure the reproducible formation of flavor substances.

Characterizing the interaction relationship of the microbial communities between Zaopei and pit mud disturbing by Daqu

The differences of interaction between interphase microbial communities were evaluated caused by two kinds of Daqu, including conventional Daqu (CDQ) and fortified Daqu (FDQ). The community diversity, functional genera and metabolites in pit mud (PM) and Zaopei (ZP) were investigated by polyphasic detecting approaches. FDQ evolved the core microbial community fitting Baijiu brewing faster than CDQ. Compared with CPM, the abundance of Aspergillus, Hyphopichia, and Penicillium in FPM were 1.54, 14.75, and 1.68 times, while that of Lactobacillus, Bacillus, Methanobrevibacter, and Methanosaeta were 2.13, 1.85, 6.35, and 3.36 times, respectively. Furthermore, the content of key flavor components was increased in ZP using FDQ. These results suggested the interaction between interphase microbial communities in various phases of Baijiu fermentation niches was significant influenced by Daqu. It can not only enhance the key volatiles in ZP but also evolve the community to fit Baijiu fermentation by introducing functional genera to Daqu.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s10068-021-00975-z.

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.

A human-food web-animal interface on the prevalence of food-borne pathogens (Clostridia and Enterococcus) in mixed veterinary farms

In the present work, we addressed the impact of a human-food web-animal interface on the prevalence of food-borne pathogens in mixed farms of Tamil Nadu, India. We have isolated and identified six strains of Clostridium sp. and five strains of Enterococcus sp. from food and animal sources disposed near to the veterinary and poultry farms. Phylogenetic relationships of these strains were inferred from their homologies in 16S rDNA sequences and rRNA secondary structures. The strain PCP07 was taxonomically equivalent to C. botulinum confirmed by neurotoxin-specific PCR primers, followed by mouse bioassay. Other Clostridial and Enterococcal isolates have shown a phylogenetic similarity to the C. bifermentans and E. durans isolated from veterinary farms, respectively. Results of our study revealed that a human-food web-animal interface has influenced the disease incidence and prevalence of these isolates in the poultry to veterinary farms, where human food acted as a likely transmittance vehicle for their infections.

Contrasting bacterial community structure in artificial pit mud-starter cultures of different qualities: a complex biological mixture for Chinese strong-flavor Baijiu production

The complex starter culture for artificial pit mud (APMSC) hosts a wide variety of microbial communities that play a crucial role in Chinese strong-flavor Baijiu production. Based on its organoleptic properties, the quality of APMSC can be divided into normal and inferior quality grades. However, the relationship between the APMSC microbial community and APMSC quality is poorly understood. In this study, the bacterial community structure in normal and inferior APMSC derived from two different production batches was analyzed using denaturing gradient gel electrophoresis and Illumina MiSeq sequencing. Highly similar patterns of bacterial diversity and community structure were observed in the APMSC samples of the same quality, and a significant higher bacterial species diversity (Shannon index and Chao1) was detected in the normal compared to the inferior APMSC samples. Fifteen genera were detected in the APMSC samples, and seven (Caproiciproducens, Clostridium, Lactobacillus, Bacillus, Pediococcus, Rummeliibacillus, and Sporolactobacillus) were dominant, accounting for 92.12-99.89% of total abundance. Furthermore, the bacterial communities in the normal and inferior APMSC had significantly different structure and function. The normal APMSC was characterized by abundant Caproiciproducens and Clostridium and high caproic and butyric acid contents. In contrast, the inferior APMSC was overrepresented by Lactobacillus and Bacillus and lactic and acetic acids. This study may help clarify the key microbes sustaining APMSC ecosystem stability and functionality, and guide future improvements in APMSC production.

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.

Deep sequencing reveals high bacterial diversity and phylogenetic novelty in pit mud from Luzhou Laojiao cellars for Chinese strong-flavor Baijiu

The pit mud (PM) in fermentation cellar is a complex ecosystem that hosts diverse microbial communities that contribute to the production of Chinese strong-flavor Baijiu (CSFB). However, the microbial ecology of PM, particularly the extent of their phylogenetic novelty remains poorly understood. Here we conducted Illumina MiSeq sequencing to explore the diversity and novelty patterns of PM bacterial communities from Luzhou Laojiao cellars in use for 40 and 400years. High diversity indices were found in the PM with 16 phyla and 105 genera. Interestingly, the compositions of dominant genera of the PM were significantly different than that reported previously for PM sampled from other geographic sites, suggesting greater microbial diversity of PM. The dominant genus of Caproiciproducens, a caproic acid-producing bacterium, is the first reported for Chinese Baijiu production. Our results demonstrate that the PM hosts a large number of novel taxa, with 26% of the total OTUs (operational taxonomic units) distant to cultured counterparts. The class Clostridia within Firmicutes presented the highest proportion of novel OTUs. Most novel OTUs were initially isolated from diverse environments, the most abundant of which came from Chinese Baijiu brewing ecosystems, highlighting the huge culturing gap within the PM, but at the same time suggesting the importance of these OTUs in CSFB production. The data presented in this study significantly increases the number of bacteria known to be associated with CSFB production and should help guide the future exploration of microbial resources for biotechnological applications.