Composition and activity of antifungal lipopeptides produced by Bacillus spp. in daqu fermentation

Regional fingerprint, enrichment and flavor contribution of Bacillus community in Daqu for Chinese Baijiu

Bacillus is an important multifunctional genus, but the enrichment and flavor contribution mechanism of this bioresource in Baijiu Daqu are still unclear. In this study, multi-omics was used to investigate the Bacillus community from the perspectives of genus, species and genes. Under the influence of fermentation process and interspecific interactions, Daqu samples from different areas will form regional Bacillus "fingerprints". The succession process and enrichment efficiency of Bacillus in high-temperature Daqu were mainly regulated by moisture. In the high-temperature fermentation environment, Bacillus community mainly contributed to baked aroma (pyrazines), creamy aroma (acetoin) and sauce aroma (guaiacol), but each Bacillus species metabolized different biomarkers and formed different sensory characteristics. The flavor contribution of Bacillus was influenced by both internal genes and external environment: Some strains have a deletion of the acoA/B gene, which reduces their ability to synthesize 2,3-butanediol; Bacillus subtilis had relatively lower GC content of the alsD (43.4 %), padC (39.3 %) and tdh (45.8 %) genes than other species, resulting in weaker stability under high-temperature environmental stress. This study offers novel insights into the distribution pattern and flavor contribution characteristics of different Bacillus species, while establishing a critical reference for the refined utilization of Bacillus bioresource.

Selection of Bacillus spp. as fermentation cultures for production of plant-based cheese analogues

Bacillus species are beneficial fermentation microbes that exhibit useful technological traits including the expression of extracellular amylolytic and proteolytic enzymes and antimicrobial lipopeptides. In this study, strains of Bacillus spp. were screened through genome analysis and the effect of fermentation of plant-based cheese analogues with the acidification cultures Lactococcus lactis, Lactococcus cremoris and Leuconostoc mesenteroides, and the adjunct culture Lentilactobacillus. buchneri plus Bacillus spp. was investigated. Based on genome analyses of 9 strains of Bacillus spp., B. velezensis FUA2155, B. amyloliquefaciens FUA2153, and B. subtilis FUA2114 that harbor genes encoding for amylases and proteases and lipopeptide synthases were selected for fermentation of plant cheese. Bacillus strains exhibited metabolic activity during bean germination but were inactive after acidification of the cheese matrix. The strains prolonged the mould-free storage time of plant-based cheese analogues and enhanced proteolysis. Of the three strains, only B. velezensis FUA2155 contributed to accumulation of taste-active glutamate. Lt. buchneri accelerated the inactivation of Ln. mesenteroides and enhanced the prevention against fungal contaminants in plant-based cheese analogues with bacilli at the ripening condition rH of 0.78. Taken together, this study provides evidence that the use of proteolytic strains of Bacillus in combination with the acidification cultures Lc. lactis and Lc. cremoris associated with Ln. mesenteroides and adjunct culture Lt. buchneri improved the quality of fermented plant-based cheese analogues.

The discrepancy in amino acids within high-temperature Daqu: A novel metabolic marker for the quality evaluation of Daqu

Mechanical pressing in Daqu production has introduced quality-affecting variations. Up to now, clear elucidation has not yet been applied to the mechanisms behind this phenomenon, and the determinants of Daqu quality are not yet completely excavated. For this reason, the physicochemical factors, enzyme activity, metabolites, and microbial communities were compared between the mechanical Daqu (MDQ) and traditional Daqu (TDQ) in this paper. The results showed significant differences in amino acids between MDQ and TDQ, with arginine being the key differentiator. High temperature, high moisture, and low acidity were crucial to Daqu's amino acid richness. Additionally, mechanical pressing affected core community stability. Bacillus was the primary biological factor for the discrepancy in amino acids. Further investigation indicated that arginine contributed to the reduction of lactic acid and higher alcohols in Jiupei, confirming that amino acids were potential novel markers affecting the quality of Daqu.

Microbial community assembly patterns at the species level in different parts of the medium temperature Daqu during fermentation

Medium-temperature Daqu (MT-Daqu) serves as a crucial saccharifying and fermentation agent in the production of strong-flavor Baijiu. Due to the spatial heterogeneity of solid fermentation, significant differences occurred in the fermentation state and appearance features in different parts of Daqu during fermentation. Currently, the understanding of the underlying mechanism behind this phenomenon remains limited. Here, we analyzed the microbial succession and assembly models and driving factors in different parts of MT-Daqu at the species level based on the PacBio single-molecule real-time sequencing technology. The results showed significantly different bacterial and fungal community compositions, successions, and interaction patterns in different parts of MT-Daqu. The bacterial community composition and succession model in the middle layer were similar to those in the core layer, whereas the fungal community composition and succession model in the surface layer were similar to those in the middle layer. The co-occurrence network analysis showed that microbial interaction is stronger in the middle and core layers than in the surface layer. Analyses based on both niche theory and neutral theory models indicated that deterministic processes predominantly governed the microbial community assembly and these processes played an increasingly important role from the surface to the core layer. Random forest analysis revealed that temperature was the primary endogenous factor driving the bacterial and fungal community assembly. The results of this study contribute to a better understanding of the microbial community in MT-Daqu and are helpful for the quality control of MT-Daqu fermentation.

Unveiling the synthesis of aromatic compounds in sauce-flavor Daqu from the functional microorganisms to enzymes

Aromatic compounds serve as the primary source of floral and fruity aromas in sauce-flavor (Maotai flavor) baijiu, constituting the skeleton components of its flavor profile. Nevertheless, the formation mechanism of these compounds and key aroma-producing enzymes in sauce-flavor Daqu (fermentation agent, SFD) remain elusive. Here, we combined metagenomics, metaproteomics, metabolomics, and key enzyme activity to verify the biosynthesis pathway of aromatic compounds and to identify key enzymes, genes, and characteristic microorganisms in SFD. The results showed that the later period of fermentation was critical for the generation of aromatic compounds in SFD. In-situ verification was conducted on the potential key enzymes and profiles in various metabolites, providing comprehensive evidence for the main synthetic pathways of aromatic compounds in SFD. Notably, our results showed that primary amine oxidase (PrAO) and aldehyde dehydrogenase (ALDH) emerged as two key enzymes promoting aromatic compound synthesis. Additionally, two potential key functional genes regulating aromatics generation were identified during SFD fermentation through correlation analysis between proteins and relevant metabolites, coupled with in vitro amplification test. Furthermore, original functional strains (Aspergillus flavus-C10 and Aspergillus niger-IN2) exhibiting high PrAO and ALDH production were successfully isolated from SFD, thus validating the results of metagenomics and metaproteomics analyses. This study comprehensively elucidates the pathway of aromatic compound formation in SFD at the genetic, proteomic, enzymatic, and metabolomic levels, providing new ideas for the investigation of key flavor substances in baijiu. Additionally, these findings offer valuable insights into the regulatory mechanisms of aromatic compounds generation.

Production, characterization, and potential applications of lipopeptides in food systems: A comprehensive review

Lipopeptides are a class of lipid-peptide-conjugated compounds with differing structural features. This structural diversity is responsible for their diverse range of biological properties, including antimicrobial, antioxidant, and anti-inflammatory activities. Lipopeptides have been attracting the attention of food scientists due to their potential as food additives and preservatives. This review provides a comprehensive overview of lipopeptides, their production, structural characteristics, and functional properties. First, the classes, chemical features, structure-activity relationships, and sources of lipopeptides are summarized. Then, the gene expression and biosynthesis of lipopeptides in microbial cell factories and strategies to optimize lipopeptide production are discussed. In addition, the main methods of purification and characterization of lipopeptides have been described. Finally, some biological activities of the lipopeptides, especially those relevant to food systems along with their mechanism of action, are critically examined.

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

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

Bioturbation analysis of microbial communities and flavor metabolism in a high-yielding cellulase Bacillus subtilis biofortified Daqu

In this study, a fortified Daqu (FF Daqu) was prepared using high cellulase-producing Bacillus subtilis, and the effects of in situ fortification on the physicochemical properties, flavor, active microbial community and metabolism of Daqu were analyzed. The saccharification power, liquefaction power, and cellulase activity of the FF Daqu were significantly increased compared with that of the traditional Daqu (CT Daqu). The overall differences in flavor components and their contents were not significant, but the higher alcohols were lower in FF Daqu. The relative abundance of dominant active species in FF Daqu was 85.08% of the total active microbiota higher than 63.42% in CT Daqu, and the biomarkers were Paecilomyces variotii and Aspergillus cristatus, respectively. The enzymes related to starch and sucrose metabolic pathways were up-regulated and expressed in FF Daqu. In the laboratory level simulation of baijiu brewing, the yield of baijiu was increased by 3.36% using FF Daqu.

Starter Culture Development and Innovation for Novel Fermented Foods

Interest in fermented foods is increasing because fermented foods are promising solutions for more secure food systems with an increased proportion of minimally processed plant foods and a smaller environmental footprint. These developments also pertain to novel fermented food for which no traditional template exists, raising the question of how to develop starter cultures for such fermentations. This review establishes a framework that integrates traditional and scientific knowledge systems for the selection of suitable cultures. Safety considerations, the use of organisms in traditional food fermentations, and the link of phylogeny to metabolic properties provide criteria for culture selection. Such approaches can also select for microbial strains that have health benefits. A science-based approach to the development of novel fermented foods can substantially advance their value through more secure food systems, food products that provide health-promoting microbes, and the provision of foods that improve human health.

Use of Bacillus spp. as beneficial fermentation microbes in baking

The development of minimally processed baked goods is dependent on new "clean label" functional ingredients that allow substitution of additives without compromising quality. We investigated the use of fermentation with Bacillus spp. as a novel approach to improve bread quality. Bacillus velezensis FUA2155 and Bacillus amyloliquefaciens Fad WE ferments were prepared using white wheat flour, wheat bran or buckwheat, and were added at a level of 2.5-20 % to bread dough. Ropy spoilage of bread was controlled by sourdough addition at a level of 10 or 20 %. The volume of white wheat bread and wheat bran bread increased by 47.4 and 62.5 % respectively with 2.5 % Bacillus ferments. Bread shelf-life was prolonged by the Bacillus ferment only at higher dosages that also reduced bread volume. The use of unfermented or sourdough fermented buckwheat improved bread volume and delayed mould spoilage. The characterization of water-soluble polysaccharides from sourdoughs and Bacillus ferments revealed that solubilization of arabinoxylans contributed to the increase in volume after fermentation of wheat but not after fermentation of buckwheat. In conclusion, Bacillus fermentation can be used to improve bread quality, adding to the diversity of microbes that are suitable for baking applications.

The effect of seed germination and Bacillus spp. on the ripening of plant cheese analogs

Consumer demand for plant cheeses is increasing, but challenges of improving both flavor and quality remain. This study investigated the microbiological and physicochemical impact of seed germination and fermentation with Bacillus velezensis and Bacillus amyloliquefaciens on the ripening of plant cheese analogs. Chlorine treatment or addition of Lactiplantibacillus plantarum and Lactococcus lactis controlled microbial growth during seed germination. Lp. plantarum and Lc. lactis also served as starter cultures for the acidification of soy and lupine milk and were subsequently present in the unripened plant cheese as dominant microbes. Acidification also inhibited the growth and metabolic activity of bacilli but Bacillus spores remained viable throughout ripening. During plant cheese ripening, Lc. lactis was inactivated before Lp. plantarum and the presence of bacilli during seed germination delayed Lc. lactis inactivation. Metagenomic sequencing of full-length 16S rRNA gene amplicons confirmed that the relative abundance of the inoculated strains in each ripened cheese sample exceeded 99%. Oligosaccharides including raffinose, stachyose, and verbascose were rapidly depleted in the initial stage of ripening. Both germination and the presence of bacilli during seed germination had impact on polysaccharide hydrolysis during ripening. Bacilli but not seed germination enhanced proteolysis of plant cheese during ripening. In conclusion, the use of germination with lactic acid bacteria in combination with Bacillus spp. exhibited the potential to improve the quality of ripened plant cheeses with a positive effect on the reduction of hygienic risks.

IMPORTANCE

The development of novel plant-based fermented food products for which no traditional templates exist requires the development of starter cultures. Although the principles of microbial flavor formation in plant-based analogs partially overlap with dairy fermentations, the composition of the raw materials and thus likely the selective pressure on the activity of starter cultures differs. Experiments that are described in this study explored the use of seed germination, the use of lactic acid bacteria, and the use of bacilli to reduce hygienic risks, to acidify plant milk, and to generate taste-active compounds through proteolysis and fermentative conversion of carbohydrates. The characterization of fermentation microbiota by culture-dependent and culture-independent methods also confirmed that the starter cultures used were able to control microbial communities throughout 90 d of ripening. Taken together, the results provide novel tools for the development of plant-based analogs of fermented dairy products.

Lipopeptides from Bacillus: unveiling biotechnological prospects-sources, properties, and diverse applications

Bacillus sp. has proven to be a goldmine of diverse bioactive lipopeptides, finding wide-range of industrial applications. This review highlights the importance of three major families of lipopeptides (iturin, fengycin, and surfactin) produced by Bacillus sp. and their diverse activities against plant pathogens. This review also emphasizes the role of non-ribosomal peptide synthetases (NRPS) as significant enzymes responsible for synthesizing these lipopeptides, contributing to their peptide diversity. Literature showed that these lipopeptides exhibit potent antifungal activity against various plant pathogens and highlight their specific mechanisms, such as siderophore activity, pore-forming properties, biofilm inhibition, and dislodging activity. The novelty of this review comes from its comprehensive coverage of Bacillus sp. lipopeptides, their production, classification, mechanisms of action, and potential applications in plant protection. It also emphasizes the importance of ongoing research for developing new and enhanced antimicrobial agents. Furthermore, this review article highlights the need for future research to improve the production efficiency of these lipopeptides for commercial applications. It recognizes the potential for these lipopeptides to expand the field of biological pest management for both existing and emerging plant diseases.

Contribution of microorganisms from pit mud to volatile flavor compound synthesis in fermented grains for nongxiangxing baijiu brewing

BACKGROUND

Nongxiangxing baijiu (NB) is known for its distinct flavor profile, which is attributed to key aroma compounds. The exposed fermentation technique, utilizing daqu and solid-state fermentation in pit muds, plays a crucial role in flavor development. Though previous studies have investigated the impact of microorganisms from pit ?ud and fermented grains on flavor compound production, a comprehensive understanding of microbial functions in the entire pit fermentation system is lacking. Herein, we aimed to explore the role of pit-mud-derived microorganisms in shaping the microbial community and flavor compound synthesis in NB.

RESULTS

There are 76 volatile flavor compounds that have been identified in fermented grains during NB fermentation. The main flavor compounds in NB clustered within the same network module, and 27.27% of microorganisms in the core modules of the fermented grain co-occurrence network originated from pit mud. The relationship between pit mud microorganisms and flavor compounds revealed a significant positive correlation (92%). Notably, Prevotella and Sarocladium were identified as the main contributors to this effect on flavor.

CONCLUSION

Microorganisms originating from pit mud influenced the composition and activity of microorganisms in fermented grains and facilitated the production of flavor compounds in NB. © 2023 Society of Chemical Industry.

Synthesis of silver nanoparticles using Bacillus velezensis M3-7 lipopeptides: Enhanced antifungal activity and potential use as a biocontrol agent against Fusarium crown rot disease of wheat seedlings

Bacillus velezensis M3-7 is a hyperactive mutant, 12-fold improved in its antifungal activity, obtained during a previous study from the wild strain BLB371 after a combination of random mutagenesis and medium component optimization. This study explores the use of this mutant in synthesizing silver nanoparticles (Ag-NPs) for the control of Fusarium crown rot disease (FCR) in wheat seedlings. LC-MS/MS analysis proved that both strains co-produced different families of lipopeptides and that mutagenesis caused the hyper-production of iturin A C14 and C15, the liberation of iturin A C10 and C12, and the inhibition of fengycin release. Our aim was a further improvement in the antifungal activity of the wild strain and the mutant M3-7 in order to control Fusarium crown rot disease (FCR) in wheat seedlings. Therefore, a nanotechnology approach was adopted, and different lipopeptide concentrations produced by the wild strain and the mutant M3-7 were used as capping agents to synthesize silver nanoparticles (Ag-NPs) with enhanced antifungal activity. Ag-NPs formed using 3 mg·mL-1 of the mutant lipopeptides were found to exhibit a good distribution, improved antifungal activity, a promising potential to be used as a biofortified agent for seed germination, and an effective compound to control FCR in wheat seedlings.

Cu (II)-catalyzed: synthesis of imidazole derivatives and evaluating their larvicidal, antimicrobial activities with DFT and molecular docking studies

This paper deals with the evaluation of novel imidazole molecules for their antimicrobial and larvicidal activities. A series of imidazole derivatives 1(a-f) and 2(a-e) were prepared by the Mannich base technique using a Cu(II) catalyst. The Cu(phen)Cl2 catalyst was found to be more effective than other methods. FTIR, elemental analyses, mass spectrometry, 1H NMR, and 13C NMR spectroscopy were performed to elucidate the structures of the synthesised compounds. Antimicrobial and larvicidal activities were investigated for all compounds. The antibacterial activity of compounds (2d) and (2a) were highly active in S.aureus (MIC: 0.25 μg/mL) and K.pneumoniae (MIC: 0.25 μg/mL) compared to ciprofloxacin. Compound (1c) was significantly more effective than clotrimazole in C.albicans (MIC: 0.25 μg/mL). Molecular docking studies of compound 2d showed a higher binding affinity for the 1BDD protein (- 3.4 kcal/mol) than ciprofloxacin (- 4.4 kcal/mol). Compound 1c had a higher binding affinity (- 6.0 kcal/mol) than clotrimazole (- 3.1 kcal/mol) with greater frontier molecular orbital energy and reactivity properties of compound 1c (∆E gap = 0.13 eV). The activity of compound 1a (LD50: 34.9 μg/mL) was more effective in the Culex quinquefasciatus than permethrin (LD50: 35.4 μg/mL) and its molecular docking binding affinity for 3OGN protein (- 6.1 kcal/mol). These newly synthesised compounds can act as lead molecules for the development of larvicides and antibiotic agents.

The active synergetic microbiota with Aspergillus as the core dominates the metabolic network of ester synthesis in medium-high temperature Daqu

The active ester-synthesis microorganisms in medium-high temperature Daqu (MHT-Daqu) largely impact the strong-flavor Baijiu quality, while their actual composition and metabolic mechanism remain unclear. Here, to explore how the active microbiota contributes to MHT-Daqu ester biosynthesis, metatranscriptomic and metaproteomic analyses coupled with experimental verification were performed. The results showed that the MHT-Daqu microbiota with the higher ester-forming ability exhibited a more active dynamic alteration from transcription to translation. The genera Aspergillus, Bacillus, Leuconostoc, and Pediococcus could transcribe and translate obviously more ester-forming enzymes. In the ester-synthesis metabolic network, the synergetic microbiota confirmed by interaction analysis, containing Eurotiales, Bacillales, and Saccharomycetales, played an essential role, in which the Eurotiales and its representative genus Aspergillus contributed the highest transcript and protein abundance in almost every metabolic process, respectively. The recombined fermentation verified that their corresponding genera could produce the ester and precursor profiles very close to that of the original MHT-Daqu active microbiota, while the microbiota without Aspergillus caused a polar separation. These results indicated that the synergetic microbiota with Aspergillus as the core dominated the metabolic network of ester synthesis in MHT-Daqu. Our study provides a detailed framework of the association between the active synergetic microbiota and ester synthesis in MHT-Daqu.

Species-Level Monitoring of Key Bacteria in Fermentation Processes Using Single-Nucleotide Resolved Nucleic Acid Assays Based on CRISPR/Cas12

Microorganisms can determine the flavor and quality of fermented food, such as Baijiu, which is produced via Daqu fermentation. Therefore, monitoring key microorganisms during fermentation is important for ensuring high-quality fermented food. Here, we report a single-nucleotide resolved nucleic acid assay based on the CRISPR/Cas12 system, enabling the quantification of Bacillus amyloliquefaciens, a key microorganism in Daqu fermentation at the species level. The assay employs an amplification-refractory mutation system derived from PCR to analyze minor genetic differences between different Bacillus species. The utilization of CRISPR/Cas12 further guaranties the specificity of identifying the PCR amplicon and enables the quantification of Bacillus amyloliquefaciens via end-measurement fluorescence. Compared to conventional qPCR, the assay allows for species-level detection of bacteria, thus enabling the precise detection of the Bacillus strain that yields high-level 2,3,5,6-tetramethylpyrazine. The assay promises the precise monitoring of bacterial growth and contribution to flavor during Daqu fermentation, thus facilitating fermented food quality control.

Enhancing fengycin production in the co-culture of Bacillus subtilis and Corynebacterium glutamicum by engineering proline transporter

Fengycin possesses antifungal activity but has limited application due to its low yields. Amino acid precursors play a crucial role in fengycin synthesis. Herein, the overexpression of alanine, isoleucine, and threonine transporter-related genes in Bacillus subtilis increased fengycin production by 34.06%, 46.66%, and 7.83%, respectively. Particularly, fengycin production in B. subtilis reached 871.86 mg/L with the addition of 8.0 g/L exogenous proline after enhancing the expression of the proline transport-related gene opuE. To overcome the metabolic burden caused by excessive enhancement of gene expression for supplying precursors, B. subtilis and Corynebacterium glutamicum which produced proline, were co-cultured, which further improved fengycin production. Fengycin production in the co-culture of B. subtilis and C. glutamicum in shake flasks reached 1554.74 mg/L after optimizing the inoculation time and ratio. The fengycin level in the fed-batch co-culture was 2309.96 mg/L in a 5.0-L bioreactor. These findings provide a new strategy for improving fengycin production.

Quorum sensing-mediated microbial interactions: Mechanisms, applications, challenges and perspectives

Microbial community in natural or artificial environments playes critical roles in substance cycles, products synthesis and species evolution. Although microbial community structures have been revealed via culture-dependent and culture-independent approaches, the hidden forces driving the microbial community are rarely systematically discussed. As a mode of cell-to-cell communication that modifies microbial interactions, quorum sensing can regulate biofilm formation, public goods secretion, and antimicrobial substances synthesis, directly or indirectly influencing microbial community to adapt to the changing environment. Therefore, the current review focuses on microbial community in the different habitats from the quorum sensing perspective. Firstly, the definition and classification of quorum sensing were simply introduced. Subsequently, the relationships between quorum sensing and microbial interactions were deeply explored. The latest progressives regarding the applications of quorum sensing in wastewater treatment, human health, food fermentation, and synthetic biology were summarized in detail. Finally, the bottlenecks and outlooks of quorum sensing driving microbial community were adequately discussed. To our knowledge, this current review is the first to reveal the driving force of microbial community from the quorum sensing perspective. Hopefully, this review provides a theoretical basis for developing effective and convenient approaches to control the microbial community with quorum sensing approaches.