Prebiotic, Probiotic, Antimicrobial, and Functional Food Applications of Bacillus amyloliquefaciens

Isolation and Characterization of a Bacillus amyloliquefaciens Bacteriophage JBA6 and Its Endolysin PlyJBA6

Bacillus amyloliquefaciens is a Gram-positive, aerobic, spore-forming bacteria usually found in soil. Despite its probiotic potential, B. amyloliquefaciens has been identified as a cause of food spoilage, including the development of off-odors, rope formation, and the production of viscous substances in a wide range of foods. To control B. amyloliquefaciens, we isolated three B. amyloliquefaciens bacteriophages TBA3, JBA3, JBA6, and characterized one representative JBA6 endolysin, PlyJBA6. Transmission electron microscopy and genomic analysis demonstrated that all three phages belong to the Salasmaviridae family, characterized by short, non-contractile tails with linear dsDNA genomes ranging from 18.7 to 19.1 kb. PlyJBA6 contains a glycoside hydrolase family 24 domain (PF00959) at the N-terminus and two LysM domains (PF04176) at the C-terminus. While JBA6 has a narrow host range, infecting only 7 out of 9 tested strains of B. amyloliquefaciens, PlyJBA6 exhibits extended lytic range beyond the Bacillus genus. Interestingly, PlyJBA6 lyses Gram-negative bacteria such as Escherichia coli, Yersinia enterocolitica and Cronobacter sakazakii without other additives to destabilize bacterial outer membrane. We assume that JBA6 might be a useful component for a phage cocktail to control B. amyloliquefaciens and that PlyJBA6 can provide insights into the development of novel biocontrol agents against various food-borne pathogens.

Antihypertensive effects of rice peptides involve intestinal microbiome alterations and intestinal inflammation alleviation in spontaneously hypertensive rats

Gut dysbiosis serves as an underlying risk factor for the development of hypertension. The resolution of this dysbiosis has emerged as a promising strategy in improving hypertension. Food-derived bioactive protein peptides have become increasingly more attractive in ameliorating hypertension, primarily due to their anti-inflammatory and anti-oxidant activities. However, the regulatory mechanisms linking rice peptides (RP), gut dysbiosis, and hypertension remain to be fully elucidated. In our study, male spontaneously hypertensive rats (SHR) were fed with chow diet and concomitantly treated with ddH2O (Ctrl) or varying doses of rice peptides (20, 100, or 500 mg (kg bw day)-1 designated as low-dose RP, LRP; medium-dose RP, MRP; high-dose RP, HAP) or captopril (Cap) by intragastric administration. Wistar-Kyoto (WKY) rats served as the normotensive control group and were orally administered with ddH2O. We observed beneficial effects of RP in lowering blood pressure and ameliorating cardiovascular risk profiles, as evidenced by improvements in glucolipid metabolic disorders, hepatic and renal damage, left ventricular hypertrophy and endothelial dysfunction in hypertensive rats. More importantly, we found that RP attenuated intestinal pathological damage, improved impaired intestinal barrier, and reduced intestinal inflammation by inhibiting the HMGB1-TLR4-NF-κB pathway. Notably, multi-omics integrative analyses have revealed that RP altered the composition and function of the gut microbiota. This is exemplified by the observed enrichment of beneficial bacterial constituents, such as g_Lactobacillus, g_Lactococcus, s_Lactobacillus_intestinalis, and Lactococcus lactis, and elevated production of microbiota-derived short-chain fatty acid metabolites. Collectively, these studies suggest that the hypotensive effects of RP may be associated with modulation of the gut microbiota and its short-chain fatty acids metabolites. This implicates the microbiota-gut-HMGB1-TLR4-NF-κB axis as a novel venue for the amelioration of hypertension and its complications.

Dynamic Changes in Physicochemical Properties and Microbial Diversity During the Fermentation of Mao-Tofu

Mao-tofu is famous for its unique flavour and texture in Anhui Province, China. The physicochemical properties and microbial diversity of Mao-tofu during different fermentation periods were studied. The pH of the tofu was acidic, the moisture gradually decreased, and the hardness, viscosity, and chewiness gradually increased, while the elasticity gradually decreased. Among these, changes in volatiles and synergistic effects of proteins, peptides, and free amino acids (FAAs) affect the flavour of Mao-tofu. Histamine had the highest concentration among all biogenic amine (BA) during the whole fermentation process. A microbial community analysis showed that Lactobacillus and Trichosporon were the most important strains throughout the fermentation process. Bacterial abundance and diversity also showed a gradual increase, while fungal abundance and diversity showed a gradual decrease. A comprehensive analysis of the physicochemical changes associated with microbial succession can help to gain insights into the maturation process of texture and flavour during the production of Mao-tofu.

Bacillus amyloliquefaciens WF2020 isolated from fermented pickles promotes longevity and health in Caenorhabditis elegans via JNK and p38 MAPK pathways

Bacillus amyloliquefaciens, a potential probiotic for use in food and feed production, can exert anti-aging effects in a strain-specific manner. However, the molecular mechanisms underlying its anti-aging effects remain poorly understood. This study explored the effects of B. amyloliquefaciens WF2020 (WF2020), isolated from Chinese fermented pickles, on longevity and health and investigated the underlying mechanisms in Caenorhabditis elegans. Interestingly, WF2020 was found to increase mean lifespan, worm length, body bends, and resistance to heat, oxidative stress, and Staphylococcus aureus infection. It also improved mitochondrial transmembrane potential and antioxidative status, reduced lipid accumulation and oxidative damage, and altered the expression of several genes involved in cell apoptosis, fat metabolism, host tolerance to heat and oxidative stress, and immune responses, compared to Escherichia coli OP50 (OP50), a standard food source for C. elegans. Moreover, WF2020-fed loss-of-function mutants for nsy-1, sek-1, pmk-1, jkk-1, jnk-1, daf-16, and hsf-1 did not exhibit lifespan extension. Additionally, WF2020-fed pmk-1 and jnk-1 mutants showed similar worm length, body bends, lipid accumulation, mitochondrial transmembrane potential, and antioxidative properties to the OP50 group. Correspondingly, WF2020 significantly upregulated the expression of nsy-1, sek-1, pmk-1, jkk-1, and jnk-1 and increased the proportion of DAF-16::GFP in the nucleus, along with the expression of HSP-16.2::GFP. In conclusion, WF2020 activated the p38 MAPK and JNK pathways to regulate the functions of HSF-1 and DAF-16, thereby promoting longevity and health in C. elegans. These findings suggest that WF2020 could be a potential probiotic or a starter for use in food and feed production to delay aging and promote health.

Changes in functional activities and volatile flavor compounds of fermented mung beans, cowpeas, and quinoa started with Bacillus amyloliquefaciens SY07

In this work, the functional activities including α-glucosidase, α-amylase, angiotensin converting enzyme (ACE) inhibitory activity, and antioxidant activity of mixed grains (mung beans, cowpeas, and quinoa) fermented with Bacillus amyloliquefaciens SY07 were investigated. The volatile flavor of the mixed grains collected every 12 h during 72 h-fermentation were further detected as well. The inhibition on α-glucosidase and α-amylase reached up to 89.34 % and 50.03 % with the sample concentration of 5.17 and 9.38 mg/mL, respectively. Moreover, the ACE inhibitory activity reached to 93.66 % with the sample concentration of 0.59 mg/mL. The antioxidant capacity of the mixed grains, evaluated by ABTS and DPPH radical scavenging capacities and ferric ion reducing power, was also significantly improved (p < 0.05) during fermentation. The maximum of ABTS and DPPH radical scavenging capacities increased to 8.64 and 3.21 mg TE/g DW, respectively, and the maximum ferric ion reducing power reached to 5.73 mg TE/g DW. Twenty-one volatile flavor compounds with odor activity values (OAVs) ≥ 1 were detected, and six key volatile flavor substances were identified by OPLS-DA analysis, namely, isovaleric acid, acetoin, phenylacetic acid, (Z)-2-nonenol, 1-hexanol, and 1-octen-3-ol, with overall strong creamy, sweet, baked-potato, and cocoa flavors upon fermentation. These findings revealed a favorable pathway for B. amyloliquefaciens SY07 to be used to improve the functional and flavor properties of fermented grains, which would also be of great value for further elucidating the mechanism of the formation of the volatile flavor differences and developing novel quality cereal-based products.

Quorum sensing: the "switch" in the competitive relationship between Gram-positive bacteria based on transcriptomic analysis

Competition phenomenon is widely presented in nature, however, few reports on the competition phenomenon between bacteria based on the perspective of quorum sensing (QS), especially between Gram-positive bacteria. Here, the Gram-positive bacteria Rhodococcus sp. HD1 and Microbacterium sp. HM-2 were co-cultured, and the epiphysiological indicators, transcriptomics combined with gene engineering technique were applied to clarify the role of QS in the competition between Gram-positive bacteria. The results showed that the morphology of strain HD1 was changed into ellipsoids from long rods, the surface-to-volume ratio increased, and the competition index increased within strains HM-2 and HD1. The biomass of strain HD1(8.06×107 CFU/mL) was decreased significantly (p＜0.05) under co-culture system, compared with mono-culture (5.75×108 CFU/mL), indicating that strain HM-2 had an inhibitory effect on HD1 at 12 h. Transcriptomic analysis revealed that QS-related genes were highly expressed in strain HM-2, and the expression level of the virulence gene TM_0352 was the highest (FPKM: 1774.19). Meanwhile, the ABC transporters-related genes in strain HD1 were significantly increased. Furthermore, QS pathway-related genes in strain HM-2 and ABC transporters-related genes in strain HD1 showed a significant correlation with the gene TM_0352 expression by the Mantel test analysis (p<0.05), surmising that the TM_0352 gene played a dominant role in the co-culture system. Knockout and complementation experiments confirmed that the function of gene TM_0352. The structural equation model showed that the QS up-regulation of strain HM-2 significantly promoted the expression of virulence genes, while strain HD1 promoted ABC transporters to cope with the up-regulation of TM_0352. The up-regulation of TM_0352 promoted the biomass of strain HM-2 and inhibited the biomass of HD1.The above results displayed that the competition phenomenon appeared by QS driving the up-regulation of TM_0352 gene in strain HM-2, which led to the up-regulation of ABC transporters in strain HD1. And these findings provided new insights into the perspective of factors related to competition inhibition between bacteria.

Cell immobilization for enhanced milk clotting enzyme production from Bacillus amyloliquefacien and cheese quality

BACKGROUND

Milk clotting enzymes, essential for milk coagulation in cheese production, are obtained from the stomach of young ruminants, an expensive and limited source. This study was accomplished by finding a suitable alternative. Bacterial isolates recovered from honey were screened for milk clotting enzyme activity. and further, by immobilization of the microorganisms to enhance stability and facilitate their repeated use.

RESULT

The most effective enzyme was produced by a microbe identified as Bacillus amyloliquefaciens based on 16 S rRNA sequencing. The cells were encapsulated in Ca2+ alginate beads. These beads retained complete enzyme production after being used five times. Glucose and Soybean were selected as the most favorable carbon and nitrogen sources, respectively. The optimum temperature for activity was 35 ℃ for both free and immobilized cells but as the temperature was increased to 55 °C and above, the encapsulated form retained more activity than the free cells. The pH optimum shifted from 6.5 to 7 for the free cells to 7-7.5 for the immobilized cells. The immobilization process decreased the activation energy for enzyme production and activity, prolonged the enzyme half-life, and increased the deactivation energy. Enzyme produced by immobilized cells generated a more compact cheese.

CONCLUSIONS

The finding of this study was to identify a less expensive source of milk-clotting enzymes and confirm the success of cell immobilization in improving cell rigidity and stability. Also, immobilization of this B. amyloliquefaciens strain offers an enzyme source of value for industrial production of cheese.

Multi-omics analyses of Bacillus amyloliquefaciens treated mice infected with Schistosoma japonicum reveal dynamics change of intestinal microbiome and its associations with host metabolism

BACKGROUND

Schistosomiasis japonica is a serious threat to human health. It causes damage to the intestine and liver. Probiotic therapy has been shown to be effective in alleviating intestinal diseases and improving host health. Previous studies have found that Bacillus amyloliquefaciens could alleviate the pathological symptoms of schistosomiasis japonica, but the regulatory mechanism of alleviating schistosomiasis japonica is still unknown.

PRINCIPAL FINDINGS

This study analyzed the dynamic changes of intestinal microbiome in mice infected with Schistosoma japonicum after the intervention of B. amyloliquefaciens and its connection to host metabolism by multi-omics sequencing technology. B. amyloliquefaciens was found to significantly regulate the homeostasis of intestinal microbiota by promoting the growth of beneficial bacteria and inhibiting potential pathogenic bacteria and protect the number of core microbes. Meanwhile, the genes related to the metabolism of glycerophospholipids and amino acid from intestinal microbiome changed significantly, and were shown to be significantly positively correlated with the associated metabolites of microbial origin. Moreover, host metabolism (lipid metabolism and steroid hormone biosynthesis) was also found to be significantly regulated.

CONCLUSIONS

The recovery of intestinal microbial homeostasis and the regulation of host metabolism revealed the potential probiotic properties of B. amyloliquefaciens, which also provided new ideas for the prevention and adjuvant treatment of schistosomiasis japonica.

The structural properties of "Huilou" yam starch fermented with five microbial species

In this study, we employed two lactic acid bacterial species, two yeast species, and Bacillus amyloliquefaciens to ferment "Huilou" yam starch. The aim was to explore the effects of fermentation time and microbial species on the structural properties of yam starch. The results showed that fermentation caused an increase in relative crystallinity (29.23 %-37.98 %) compared with native starch (25.69 %). The fermentation process altered the thermal properties of yam starch, leading to higher enthalpy of gelatinization values compared with unfermented starch. Notably, an absorption peak of native starch shifted from 992 cm-1 to 1015 cm-1 upon 2-day fermentation by Bacillus amyloliquefaciens and 5-day fermentation by Lactobacillus plantarum or Pediococcus pentococcus, associated with an increase in the presence of amorphous structures in yam starch. "Huilou" yam starch obtained through lactic acid bacterial fermentation exhibited a significant presence of organic acids, whereas samples derived from Bacillus amyloliquefaciens fermentation were primarily affected by amylase activity. Following yeast fermentation, organic acids and amylase were observed, albeit with relatively low influence. This research reveals that microbial fermentation can potentially alter the structural characteristics of yam starch, which can improve the quality of yam starch-based foods.

Novel misos shape distinct microbial ecologies: opportunities for flavourful sustainable food innovation

Fermentation is resurgent around the world as people seek healthier, more sustainable, and tasty food options. This study explores the microbial ecology of miso, a traditional Japanese fermented paste, made with novel regional substrates to develop new plant-based foods. Eight novel miso varieties were developed using different protein-rich substrates: yellow peas, Gotland lentils, and fava beans (each with two treatments: standard and nixtamalisation), as well as rye bread and soybeans. The misos were produced at Noma, a restaurant in Copenhagen, Denmark. Samples were analysed with biological and technical triplicates at the beginning and end of fermentation. We also incorporated in this study six samples of novel misos produced following the same recipe at Inua, a former affiliate restaurant of Noma in Tokyo, Japan. To analyse microbial community structure and diversity, metabarcoding (16S and ITS) and shotgun metagenomic analyses were performed. The misos contain a greater range of microbes than is currently described for miso in the literature. The composition of the novel yellow pea misos was notably similar to the traditional soybean ones, suggesting they are a good alternative, which supports our culinary collaborators' sensory conclusions. For bacteria, we found that overall substrate had the strongest effect, followed by time, treatment (nixtamalisation), and geography. For fungi, there was a slightly stronger effect of geography and a mild effect of substrate, and no significant effects for treatment or time. Based on an analysis of metagenome-assembled genomes (MAGs), strains of Staphylococccus epidermidis differentiated according to substrate. Carotenoid biosynthesis genes in these MAGs appeared in strains from Japan but not from Denmark, suggesting a possible gene-level geographical effect. The benign and possibly functional presence of S. epidermidis in these misos, a species typically associated with the human skin microbiome, suggests possible adaptation to the miso niche, and the flow of microbes between bodies and foods in certain fermentation as more common than is currently recognised. This study improves our understanding of miso ecology, highlights the potential for developing novel misos using diverse local ingredients, and suggests how fermentation innovation can contribute to studies of microbial ecology and evolution.

Fermentation of DaiDai fruit and its biological activity

DaiDai fruit, a medicinal and edible plant fruit, is abundant in biologically active compounds and has a long history of use in traditional Chinese medicine. This research focuses on utilizing fermentation to develop a functional DaiDai fruit fermentation broth. Lactobacillus, Bacillus subtilis and Saccharomyces cerevisiae were employed in the fermentation process. By conducting screenings of bacterial strains, single factor experiments, and response surface methodology, the total flavonoids, polysaccharides, polyphenols, and 1,1-diphenyl-2-trinitrophenylhydrazine (DPPH) free radical scavenging rate were used as the index for selection, ultimately identifying Lactobacillus L-13 as the optimal fermentation strain. The optimal fermentation conditions were determined to be a time of 108 h, a temperature of 43.6°C, and a solid-liquid ratio of 1:15.157 (w/v). Under these conditions, the total flavonoid content reached 412.01 mg/g, representing a 36.71% increase compared to conventional extraction methods. The contents of polysaccharides and polyphenols and the DPPH scavenging rate were also increased. The fermentation broth of DaiDai fruit exhibited inhibitory effects on tyrosinase and melanin production in mouse melanoma cells B16-F10 induced by α-MSH and anti-inflammatory properties in a zebrafish inflammation model. These indicate that the DaiDai fruit fermentation broth possesses anti-melanoma, whitening, and anti-inflammatory properties, showcasing significant potential for applications in medicine, cosmetics, and other industries.

Bacillus amyloliquefaciens Protect Against Atherosclerosis Through Alleviating Foam Cell Formation and Macrophage Polarization

This study was to investigate the therapeutic effect of Bacillus amyloliquefaciens (Ba) on atherosclerosis (AS). THP-1 monocyte was differentiated to THP-1 macrophage (THP-M) through phorbol 12-myristate 13-acetate. After pre-treatment by 108 cfu/ml Ba lasting 6 h, THP-M was induced with 100 mg/l ox-LDL lasting 48 h to form macrophage foam cell (THP-F). RT-qPCR and flow cytometry were employed to determine the polarization of THP-M and THP-F. ApoE-/- mice with high-fat and high-cholesterol diet were used for constructing an AS model to evaluate the effect of Ba on AS. Our in vitro results showed that Ba vegetative cells pre-treatment distinctly inhibited the levels of iNOS and CD16/CD32 (M1 macrophage markers), and increased the levels of FIZZ1, Ym1, Arg1, CD163, and CD206 (M2 macrophage markers), indicating that Ba pre-treatment promoted anti-inflammatory M2-like polarization both in THP-M and THP-F. Meanwhile, it also suppressed cholesterol uptake, esterification, and hydrolysis, and efflux by THP-M and THP-F. Additionally, our animal experiments demonstrated that Ba vegetative cells treatment suppressed high cholesterol, hyperglycemia, hyperlipidemia, and the release of inflammatory factors (TNF-α, IL-6 and IL-1β) in ApoE-/- AS mice. In a word, our results indicated that Ba may protect against AS through alleviating foam cell formation and macrophage polarization through targeting certain stages of AS.

Domestication and Genetic Improvement Alter the Symbiotic Microbiome Structure and Function of Tomato Leaf and Fruit Pericarp

Many studies have attempted to explore the changes in the structure and function of symbiotic microbiomes, as well as the underlying genetic mechanism during crop domestication. However, most of these studies have focused on crop root microbiomes, while those on leaf and fruit are rare. In this study, we generated a comprehensive dataset including the metagenomic (leaf) and metatranscriptomic (fruit pericarp in the orange stage) data of hundreds of germplasms from three tomato clades: Solanum pimpinellifolium (PIM), cherry tomato (S. lycopersicum var. cerasiforme) (CER), and S. lycopersicum group (BIG). We investigated the effect of domestication and improvement processes on the structure of the symbiotic microbiome of tomato leaf and fruit pericarp, as well as its genetic basis. We were able to obtain the composition of the symbiotic microbiome of tomato leaf and fruit pericarp, based on which the tomato clade (PIM, CER, or BIG) was predicted with high accuracy through machine learning methods. In the processes of tomato domestication and improvement, changes were observed in the relative abundance of specific bacterial taxa, Bacillus for example, in the tomato leaf and fruit pericarp symbiotic microbiomes, as well as in the function of these symbiotic microbiomes. In addition, SNP loci that were significantly associated with microbial species that are characteristic of tomato leaf were identified. Our results show that domestication and genetic improvement processes alter the symbiotic microbiome structure and function of tomato leaf and fruit pericarp. We propose that leaf and fruit microbiomes are more suitable for revealing changes in symbiotic microbiomes during the domestication process and the underlying genetic basis for these changes due to the exclusion of the influence of environmental factors such as soil types on the microbiome structure.

Harnessing Bacillus amyloliquefaciens for Amazake Production: Comparison with Aspergillus oryzae Amazake for Metabolomic Characteristics, Microbial Diversity, and Sensory Profile

Amazake is a traditional, sweet, non-alcoholic Japanese beverage typically produced through koji fermentation by the fungus Aspergillus oryzae. However, alternative microorganisms such as Bacillus amyloliquefaciens offer potential advantages and novel possibilities for producing similar fermented beverages. This study aimed to replicate the ancestral beverage of amazake by replacing A. oryzae (W-20) with B. amyloliquefaciens (NCIMB 12077) and comparing their fermentation processes and resulting products. Our results show that the production of amazake with B. amyloliquefaciens (ABA) is not only possible but also results in a beverage that is otherwise distinct from traditional amazake (AAO). Saccharification was achievable in ABA at higher temperatures than in AAO, albeit with lower reducing sugar and enzymatic activity values. Amino acids and organic acids were more abundant in AAO, with cysteine being uniquely present in AAO and shikimic acid only being present in ABA. The volatile aroma compound profiles differed between the two beverages, with AAO exhibiting a greater abundance of aldehydes, and ABA a greater abundance of ketones and alcohols. Interestingly, despite these compositional differences, the two beverages showed similar consumer panel acceptance rates. An analysis of their microbial communities revealed pronounced differences between the amazakes, as well as temporal changes in ABA but not in AAO. This study provides promising insights into harnessing the potential of B. amyloliquefaciens as the primary microorganism in the fermentation process of amazake-like beverages, marking an important advancement in the field of fermented low-alcohol beverage production, with possible applications in other fermented foods.

Metagenomic analysis of the intestinal microbiome reveals the potential mechanism involved in Bacillus amyloliquefaciens in treating schistosomiasis japonica in mice

Schistosomiasis japonica is one of the neglected tropical diseases characterized by chronic hepatic, intestinal granulomatous inflammation and fibrosis, as well as dysbiosis of intestinal microbiome. Previously, the probiotic Bacillus amyloliquefaciens has been shown to alleviate the pathological injuries in mice infected with Schistosoma japonicum by improving the disturbance of the intestinal microbiota. However, the underlying mechanisms involved in this process remain unclear. In this study, metagenomics sequencing and functional analysis were employed to investigate the differential changes in taxonomic composition and functional genes of the intestinal microbiome in S. japonicum-infected mice treated with B. amyloliquefaciens. The results revealed that intervention with B. amyloliquefaciens altered the taxonomic composition of the intestinal microbiota at the species level in infected mice and significantly increased the abundance of beneficial bacteria. Moreover, the abundance of predicted genes in the intestinal microbiome was also significantly changed, and the abundance of xfp/xpk and genes translated to urease was significantly restored. Further analysis showed that Limosilactobacillus reuteri was positively correlated with several KEGG Orthology (KO) genes and metabolic reactions, which might play important roles in alleviating the pathological symptoms caused by S. japonicum infection, indicating that it has the potential to function as another effective therapeutic agent for schistosomiasis. These data suggested that treatment of murine schistosomiasis japonica by B. amyloliquefaciens might be induced by alterations in the taxonomic composition and functional gene of the intestinal microbiome in mice. We hope this study will provide adjuvant strategies and methods for the early prevention and treatment of schistosomiasis japonica.

IMPORTANCE

Targeted interventions of probiotics on gut microbiome were used to explore the mechanism of alleviating schistosomiasis japonica. Through metagenomic analysis, there were significant changes in the composition of gut microbiota in mice infected with Schistosoma japonicum and significant increase in the abundance of beneficial bacteria after the intervention of Bacillus amyloliquefaciens. At the same time, the abundance of functional genes was found to change significantly. The abundance of genes related to urease metabolism and xfp/xpk related to D-erythrose 4-phosphate production was significantly restored, highlighting the importance of Limosilactobacillus reuteri in the recovery and abundance of predicted genes of the gut microbiome. These results indicated potential regulatory mechanism between the gene function of gut microbiome and host immune response. Our research lays the foundation for elucidating the regulatory mechanism of probiotic intervention in alleviating schistosomiasis japonica, and provides potential adjuvant treatment strategies for early prevention and treatment of schistosomiasis japonica.

Identification of marker compounds in fermented Benincasa hispida and validation of the method for its analysis

Fermentation is a process that improves health functionality by inducing the production and increase of bioactive compounds. In this study, to standardize the fermentation process for Benincasa hispida, marker compounds that are increased or produced during fermentation were identified based on UPLC-QTOF-MS/MS. Analysis method verification and content analysis were conducted using HPLC-PDA. The marker compounds produced or increased in content were identified as 2-furoic acid, 2,3-dihydroxybenzoic acid, and rubinaphthin A by comparing their retention times, UV and MS spectra, and molecular formulas with those reported in previous studies. In addition, the increase in the content of the marker compounds by fermentation was confirmed, and the analytical method was validated by measuring its specificity, linearity, limit of detection and quantitation, precision, and accuracy. These results suggest that the developed fermentation process, marker compound identification, and verified analysis method can be applied to develop potential functional food ingredients from fermented B. hispida.

Plant Growth Promotion and Plant Disease Suppression Induced by Bacillus amyloliquefaciens Strain GD4a

Botrytis cinerea, the causative agent of gray mold disease (GMD), invades plants to obtain nutrients and disseminates through airborne conidia in nature. Bacillus amyloliquefaciens strain GD4a, a beneficial bacterium isolated from switchgrass, shows great potential in managing GMD in plants. However, the precise mechanism by which GD4a confers benefits to plants remains elusive. In this study, an A. thaliana-B. cinerea-B. amyloliquefaciens multiple-scale interaction model was used to explore how beneficial bacteria play essential roles in plant growth promotion, plant pathogen suppression, and plant immunity boosting. Arabidopsis Col-0 wild-type plants served as the testing ground to assess GD4a's efficacy. Additionally, bacterial enzyme activity and targeted metabolite tests were conducted to validate GD4a's potential for enhancing plant growth and suppressing plant pathogens and diseases. GD4a was subjected to co-incubation with various bacterial, fungal, and oomycete pathogens to evaluate its antagonistic effectiveness in vitro. In vivo pathogen inoculation assays were also carried out to investigate GD4a's role in regulating host plant immunity. Bacterial extracellular exudate (BEE) was extracted, purified, and subjected to untargeted metabolomics analysis. Benzocaine (BEN) from the untargeted metabolomics analysis was selected for further study of its function and related mechanisms in enhancing plant immunity through plant mutant analysis and qRT-PCR analysis. Finally, a comprehensive model was formulated to summarize the potential benefits of applying GD4a in agricultural systems. Our study demonstrates the efficacy of GD4a, isolated from switchgrass, in enhancing plant growth, suppressing plant pathogens and diseases, and bolstering host plant immunity. Importantly, GD4a produces a functional bacterial extracellular exudate (BEE) that significantly disrupts the pathogenicity of B. cinerea by inhibiting fungal conidium germination and hypha formation. Additionally, our study identifies benzocaine (BEN) as a novel small molecule that triggers basal defense, ISR, and SAR responses in Arabidopsis plants. Bacillus amyloliquefaciens strain GD4a can effectively promote plant growth, suppress plant disease, and boost plant immunity through functional BEE production and diverse gene expression.

The Contribution of Microorganisms to the Quality and Flavor Formation of Chinese Traditional Fermented Meat and Fish Products

Guizhou sour meat and sour fish, Chaoshan fish sauce, Sichuan sausage and bacon, Cantonese sausage, Jinhua ham, and Xinjiang air-dried beef are eight representatives of Chinese traditional fermented meat and fish products (FMFPs), which are favored by Chinese consumers due to their high nutritional value and quality. The quality of the spontaneously fermented Chinese traditional FMFP is closely correlated with microorganisms. Moreover, the dominant microorganisms are significantly different due to regional differences. The effects of microorganisms on the texture, color, flavor, nutrition, functional properties, and safety of Chinese traditional FMFPs have not been not fully described. Additionally, metabolic pathways for flavor formation of Chinese traditional FMFPs have not well been summarized. This article describes the seven characteristic Chinese traditional FMFPs and correlated dominant microorganisms in different regions of China. The effects of microorganisms on the texture, color, and flavor of Chinese traditional FMFPs are discussed. Furthermore, the metabolic pathways of microbial regulation of flavor formation in Chinese traditional FMFPs are proposed. This work provides a theoretical basis for improvement of Chinese traditional FMFPs by inoculating functional microorganisms isolated from Chinese traditional fermented foods.

Probiotic Potential of Bacillus amyloliquefaciens Isolated from Tibetan Yaks

The Tibetan livestock sector is now ailing from many infectious ailments brought on by harmful microorganisms. Therefore, this research aimed to assess the probiotic potential and safety of Bacillus amyloliquefaciens isolated from yaks in the Tibet area to provide upper-edge strain resources for probiotics development. The four strains isolated from the intestine of yaks had been identified as Bacillus amyloliquefaciens after the 16S rRNA sequence. The ethanol, bile salt, and acid tolerance revealed that the isolates had significant tolerance levels. The antibiotics susceptibility assay showed that the strains were sensitive to commonly used antibiotics, while the antibacterial assay prevented the isolates from outperforming five harmful bacteria in terms of antibacterial potency. Moreover, it was evident that strain BA5 had the strongest activity to scavenge hydroxyl radical and reduce power. According to the animal experiment, no apparent pathological change was observed in intestinal tissue sections. Furthermore, the strain had a positive effect on promoting the development of jejunal villi referred to its safety. Therefore, more research is required into the bacteriostatic and antioxidant capabilities of isolates in animal production.

Exploring the microbial diversity of novel misos with metagenomics

Interest in fermented foods, especially plant-based ones, has increased considerably in the last decade. Miso-a Japanese paste traditionally fermented with soybeans, salt, and kōji (Aspergillus oryzae grown on grains or beans)-has gained attention among chefs for its rich flavour and versatility. Some chefs have even been experimenting with making novel misos with untraditional substrates to create new flavours. Such novel fermented foods also offer new scientific opportunities. To explore the microbial diversity of these new traditional foods, we sampled six misos made by the team at a leading restaurant called Noma in Copenhagen (Denmark), using yellow peas (including a nixtamalised treatment), lupin seeds, Swedish Vreta peas, grey peas, and Gotland lentils as substrates. All misos were made with the same recipe and fermented for 3 months at 28 °C. Samples were collected at the end of fermentation for subsequent shotgun metagenomic sequencing and a genome-resolved metagenomic analysis. The taxonomic profile of the samples revealed the presence of kōji mould (A. oryzae) and Bacillus amyloliquefaciens in all misos. Various species of the genera Latilactobacillus, Lactiplantibacillus, Pediococcus and Staphylococcus were also detected. The Metagenome-Assembled Genomes (MAGs) revealed genomic sequences belonging to 12 different species and functional analyses of these MAGs were performed. Notably, we detected the presence of Exiguobacterium-the first reported instance of the genus in miso-and Average Nucleotide Identity (ANI) analyses suggest a potentially new species. We hope these results will improve the scientific literature on misos and contribute to developing novel fermented plant-based foods.

Characterization of white chocolate enriched with co-encapsulated Lactobacillus acidophilus (La-5) and rose hip shell fruit extract: Characterization, probiotic viability during storage, and in vitro gastrointestinal digestion

This research focused on the production of a new kind of probiotic chocolate containing co-encapsulated Lactobacillus acidophilus (La-5) bacteria and rose hip shell fruit extract. Several properties of chocolate samples, including rheological, textural, thermal properties, particle size distribution, color indices, total phenolic and anthocyanin magnitude, antioxidant potential, and Raman spectroscopy were performed. The prepared white chocolates were assessed for the survival of the probiotic cell and the stability of anthocyanins and phenolic components in different storage times (until 90 days) and different storage temperatures (at 4 and 25°C). Observations imply that both temperature and duration of storage had an impact on the extent of survival of probiotics as well as stability of total phenolic content (TPC) and anthocyanin content (p < .05). During in vitro gastrointestinal circumstances, the extent of survival of L. acidophilus, in two chocolate matrixes, was assessed. At the end of gastric and intestinal condition, the log of viable cells was 7 and 6, respectively. The magnitude of the bioaccessibility of anthocyanin and phenolic components was 81% and 78%, respectively. Sensory evaluation affirmed that there was no remarkable variation between samples in terms of overall acceptance.

Bacillus amyloliquefaciens B10 Alleviates the Immunosuppressive Effects of Deoxynivalenol and Porcine Circovirus Type 2 Infection

As one of the most common mycotoxins, deoxynivalenol (DON) can contaminate a wide range of crops and foods. Porcine circovirus 2 (PCV2) is a kind of immunosuppressive virus, which can cause porcine circovirus associated disease (PCVD) in pig farms infected with PCV2. Pigs are extremely sensitive to DON, and PCV2-infected pig farms are often contaminated with DON. Our previous studies indicated that Bacillus amyloliquefaciens B10 (B10) has the potential to alleviate the toxicity of mycotoxins. The research was aimed at investigating the effects of Bacillus amyloliquefaciens B10 on the immunosuppressive effects caused by both DON and PCV2 infection. The results indicated that the expression of the PCV2 capsid protein CAP was significantly decreased after pretreatment with Bacillus amyloliquefaciens B10. Then, the effects of the Bacillus amyloliquefaciens B10 pretreatment on the type I interferon, antiviral protein and the antiviral signal pathway cGAS-STING was further investigated. The findings displayed that the expression of the type I interferon and antiviral protein were increased, while the IL-10 were decreased after pretreatment with Bacillus amyloliquefaciens B10. The inhibition of DON on the cGAS-STING signal pathway was relieved. Furthermore, it was found that this intervention effect was produced by inhibiting autophagy. In summary, Bacillus amyloliquefaciens B10 can mitigate the immunosuppressive effects of PCV2 and DON by inhibiting the production of autophagy.

Isolation, Antimicrobial Effect and Metabolite Analysis of Bacillus amyloliquefaciens ZJLMBA1908 against Citrus Canker Caused by Xanthomonas citri subsp. citri

Citrus canker caused by Xanthomonas citri subsp. citri is a devastating bacterial disease with severe implications for the citrus industry. Microorganisms possessing biocontrol capabilities against X. citri subsp. citri offer a highly promising strategy for healthy citrus management. In the present study, a broad-spectrum antagonist strain ZJLMBA1908 with potent antibacterial activity against X. citri subsp. citri was isolated from symptomatic lemon leaves, and identified as Bacillus amyloliquefaciens. Cell-free supernatant (CFS) of strain ZJLMBA1908 also exhibited remarkable antimicrobial activity, especially suppressing the growth of X. citri subsp. citri and Nigrospora oryzae, with inhibition rates of 27.71% and 63.75%, respectively. The antibacterial crude extract (CE) derived from the CFS displayed effective activity against X. citri subsp. citri. A preventive treatment using the CE significantly reduced the severity and incidence of citrus canker in a highly susceptible citrus host. Additionally, the CE maintained activity in the presence of protease and under a wide range of temperature and pH treatments. Applying high-performance liquid chromatography (HPLC) to separate and purify the CE resulted in the discovery of one highly potent anti-X. citri subsp. citri subfraction, namely CE3, which could completely inhibit the growth of X. citri subsp. citri. Liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS) analysis revealed that CE3 mainly consisted of palmitic acid, surfactin C15, phytosphingosine and dihydrosphingosine. Taken together, the results contribute to the possible biocontrol mechanisms of B. amyloliquefaciens ZJLMBA1908, as well as providing a promising new candidate strain as a biological control agent for controlling citrus canker.

Recent advances and prospects of Bacillus amyloliquefaciens as microbial cell factories: from rational design to industrial applications

Bacillus amyloliquefaciens is one of the most characterized Gram-positive bacteria. This species has unique characteristics that are beneficial for industrial applications, including its utilization of: cheap carbon as a substrate, a transparent genetic background, and large-scale robustness in fermentation. Indeed, the productivity characteristics of B. amyloliquefaciens have been thoroughly analyzed and further optimized through systems biology and synthetic biology techniques. Following the analysis of multiple engineering design strategies, B. amyloliquefaciens is now considered an efficient cell factory capable of producing large quantities of multiple products from various raw materials. In this review, we discuss the significant potential advantages offered by B. amyloliquefaciens as a platform for metabolic engineering and industrial applications. In addition, we systematically summarize the recent laboratory research and industrial application of B. amyloliquefaciens, including: relevant advances in systems and synthetic biology, various strategies adopted to improve the cellular performances of synthetic chemicals, as well as the latest progress in the synthesis of certain important products by B. amyloliquefaciens. Finally, we propose the current challenges and essential strategies to usher in an era of broader B. amyloliquefaciens use as microbial cell factories.

Identification and Growth Characteristics of a Gluten-Degrading Bacterium from Wheat Grains for Gluten-Degrading Enzyme Production

Immunogenic peptides from wheat gluten can be produced during digestion, which are difficult to digest by gastrointestinal proteases and negatively affect immune responses in humans. Gluten intolerance is a problem in countries where wheat is a staple food, and a gluten-free diet is commonly recommended for its treatment and prevention. Enzyme approaches for degradation of the peptides can be considered as a strategy for its prevention. Here, we isolated a gluten-degrading bacterium, Bacillus amyloliquefaciens subsp. plantarum, from wheat grains. The culture conditions for enzyme production or microbial use were considered based on gluten decomposition patterns. Additionally, the pH range for the activity of the crude enzyme was investigated. The bacterium production of gluten-degrading enzymes was temperature-dependent within 25 °C to 45 °C, and the production time decreased with increasing culture temperature. However, it was markedly decreased with increasing biofilm formation. The bacterium decomposed high-molecular-weight glutenin proteins first, followed by gliadin proteins, regardless of the culture temperature. Western blotting with an anti-gliadin antibody revealed that the bacterium decomposed immunogenic proteins related to α/β-gliadins. The crude enzyme was active in the pH ranges of 5 to 8, and enzyme production was increased by adding gliadin into the culture medium. In this study, the potential of the B. amyloliquefaciens subsp. plantarum for gluten-degrading enzyme production was demonstrated. If further studies for purification of the enzyme specific to the immunogenic peptides and its characteristics are conducted, it may contribute as a strategy for prevention of gluten intolerance.

A Probiotic Bacillus amyloliquefaciens D-1 Strain Is Responsible for Zearalenone Detoxifying in Coix Semen

Zearalenone (ZEN) is a mycotoxin produced by Fusarium spp., which commonly and severely contaminate food/feed. ZEN severely affects food/feed safety and reduces economic losses owing to its carcinogenicity, genotoxicity, reproductive toxicity, endocrine effects, and immunotoxicity. To explore efficient methods to detoxify ZEN, we identified and characterized an efficient ZEN-detoxifying microbiota from the culturable microbiome of Pseudostellaria heterophylla rhizosphere soil, designated Bacillus amyloliquefaciens D-1. Its highest ZEN degradation rate reached 96.13% under the optimal condition. And, D-1 can almost completely remove ZEN (90 μg·g-1) from coix semen in 24 h. Then, the D-1 strain can detoxify ZEN to ZEM, which is a new structural metabolite, through hydrolyzation and decarboxylation at the ester group in the lactone ring and amino acid esterification at C2 and C4 hydroxy. Notably, ZEM has reduced the impact on viability, and the damage of cell membrane and nucleus DNA and can significantly decrease the cell apoptosis in the HepG2 cell and TM4 cell. In addition, it was found that the D-1 strain has no adverse effect on the HepG2 and TM4 cells. Our findings can provide an efficient microbial resource and a reliable reference strategy for the biological detoxification of ZEN.

Bacillus velezensis ZN-S10 Reforms the Rhizosphere Microbial Community and Enhances Tomato Resistance to TPN

Tomato pith necrosis (TPN) is a highly destructive disease caused by species of the Pseudomonas genus and other bacteria, resulting in a significant reduction in tomato yield. Members of the genus Bacillus are beneficial microorganisms extensively studied in the rhizosphere. However, in most cases, the potential of Bacillus members in controlling TPN and their impact on the rhizosphere microbial composition remain rarely studied. In this study, Bacillus velezensis ZN-S10 significantly inhibited the growth of Pseudomonas viridiflava ZJUP0398-2, and ZN-S10 controlled TPN with control efficacies of 60.31%. P. viridiflava ZJUP0398-2 significantly altered the richness and diversity of the tomato rhizobacterial community, but pre-inoculation with ZN-S10 mitigated these changes. The correlation analysis revealed that ZN-S10 maybe inhibits the growth of nitrogen-fixing bacteria and recruits beneficial bacterial communities associated with disease resistance, thereby suppressing the occurrence of diseases. In summary, the comparative analysis of the rhizosphere microbiome was conducted to explore the impact of ZN-S10 on the composition of rhizosphere microorganisms in the presence of pathogenic bacteria, aiming to provide insights for further research and the development of scientific and eco-friendly control strategies for this disease.

Optimizing the Fermentation Conditions of Cudrania tricuspidata Fruit Using Bacillus amyloliquefaciens for Anti-Inflammatory Activity and GC-MS-Based Volatile Component Characteristics

The aim of this study is to optimize the performance conditions used for maximum anti-inflammatory activity and to clarify in vitroanti-inflammatory properties of fermented C. tricuspidata fruit. Based on the single-factor experiment and Box-Behnken design, the optimized fermentation conditions of C. tricuspidata fruit for maximum anti-inflammatory activity were 3.8 d fermentation period, 8.4% (v/w) inoculation concentration, and 29.2°C fermentation temperature. Under optimal conditions, anti-inflammatory activity-based nitric oxide of fermented C. tricuspidata fruit reached 93.9%. Moreover, this study provides a theoretical basis and experimental data containing β-hexosaminidase and reactive oxygen species for the medical use and industrialization of C. tricuspidata fruit fermentation. Interestingly, the results of GC-MS analysis confirmed that fermented C. tricuspidata fruits detect volatile components different from unfermented C. tricuspidata fruits. We suggested that this volatile component may have been involved in the anti-inflammatory reaction, but scientific verification of this is needed later. Therefore, an in-depth study of volatile components detected from fermented C. tricuspidata fruits will need to be conducted later.

Mining the nanotube-forming Bacillus amyloliquefaciens MR14M3 genome for determining anti-Candida auris and anti-Candida albicans potential by pathogenicity and comparative genomics analysis

There is a global health concern associated with the emergence of the multidrug-resistant (MDR) fungus Candida auris, which has significant mortality rates. Finding innovative and distinctive anti-Candida compounds is essential for treating infections caused by MDR C. auris. A bacterial strain with anti-Candida activity was isolated and identified using 16 S rRNA gene sequencing. The whole genome was sequenced to identify biosynthesis-related gene clusters. The pathogenicity and cytotoxicity of the isolate were analyzed in Candida and HFF-1 cell lines, respectively. This study set out to show that whole-genome sequencing, cytotoxicity testing, and pathogenicity analysis combined with genome mining and comparative genomics can successfully identify biosynthesis-related gene clusters in native bacterial isolates that encode antifungal natural compounds active against Candida albicans and C. auris. The native isolate MR14M3 has the ability to inhibit C. auris (zone of inhibition 25 mm) and C. albicans (zone of inhibition 25 mm). The 16 S rRNA gene sequence of MR14M3 aligned with Bacillus amyloliquefaciens with similarity (100%). Bacillus amyloliquefaciens MR14M3 establishes bridges of intercellular nanotubes (L 258.56 ± 35.83 nm; W 25.32 ± 6.09 nm) connecting neighboring cells. Candida cell size was reduced significantly, and crushed phenotypes were observed upon treatment with the defused metabolites of B. amyloliquefaciens MR14M3. Furthermore, the pathogenicity of B. amyloliquefaciens MR14M3 on Candida cells was observed through cell membrane disruption and lysed yeast cells. The whole-genome alignment of the MR14M3 genome (3981,643 bp) using 100 genes confirmed its affiliation with Bacillus amyloliquefaciens. Genome mining analysis revealed that MR14M3-coded secondary metabolites are involved in the biosynthesis of polyketides (PKs) and nonribosomal peptide synthases (NRPSs), including 11 biosynthesis-related gene clusters with one hundred percent similarity. Highly conserved biosynthesis-related gene clusters with anti-C. albicans and anti-C. auris potentials and cytotoxic-free activity of B. amyloliquefaciens MR14M3 proposes the utilization of Bacillus amyloliquefaciens MR14M3 as a biofactory for an anti-Candida auris and anti-C. albicans compound synthesizer.

Bacillus amyloliquefaciens: Harnessing Its Potential for Industrial, Medical, and Agricultural Applications-A Comprehensive Review

Bacillus amyloliquefaciens, a Gram-positive bacterium, has emerged as a versatile microorganism with significant applications in various fields, including industry, medicine, and agriculture. This comprehensive review aims to provide an in-depth understanding of the characteristics, genetic tools, and metabolic capabilities of B. amyloliquefaciens, while highlighting its potential as a chassis cell for synthetic biology, metabolic engineering, and protein expression. We discuss the bacterium's role in the production of chemicals, enzymes, and other industrial bioproducts, as well as its applications in medicine, such as combating infectious diseases and promoting gut health. In agriculture, B. amyloliquefaciens has demonstrated potential as a biofertilizer, biocontrol agent, and stress tolerance enhancer for various crops. Despite its numerous promising applications, B. amyloliquefaciens remains less studied than its Gram-negative counterpart, Escherichia coli. This review emphasizes the need for further research and development of advanced engineering techniques and genetic editing technologies tailored for B. amyloliquefaciens, ultimately unlocking its full potential in scientific and industrial contexts.

Effect of NaCl stress on exoproteome profiles of Bacillus amyloliquefaciens EB2003A and Lactobacillus helveticus EL2006H

Salt stress can affect survival, multiplication and ability of plant growth promoting microorganisms to enhance plant growth. Changes in a microbe's proteome profile is one of the mechanisms employed by PGPM to enhance tolerance of salt stress. This study was focused on understanding changes in the exoproteome profile of Bacillus amyloliquefaciens EB2003A and Lactobacillus helveticus EL2006H when exposed to salt stress. The strains were cultured in 100 mL M13 (B. amyloliquefaciens) and 100 mL De man, Rogosa and Sharpe (MRS) (L. helveticus) media, supplemented with 200 and 0 mM NaCl (control), at pH 7.0. The strains were then incubated for 48 h (late exponential growth phase), at 120 rpm and 30 (B. amyloliquefaciens) and 37 (L. helveticus) °C. The microbial cultures were then centrifuged and filtered sterilized, to obtain cell free supernatants whose proteome profiles were studied using LC-MS/MS analysis and quantified using scaffold. Results of the study revealed that treatment with 200 mM NaCl negatively affected the quantity of identified proteins in comparison to the control, for both strains. There was upregulation and downregulation of some proteins, even up to 100%, which resulted in identification of proteins significantly unique between the control or 200 mM NaCl (p ≤ 0.05), for both microbial species. Proteins unique to 200 mM NaCl were mostly those involved in cell wall metabolism, substrate transport, oxidative stress tolerance, gene expression and DNA replication and repair. Some of the identified unique proteins have also been reported to enhance plant growth. In conclusion, based on the results of the work described here, PGPM alter their exoproteome profile when exposed to salt stress, potentially upregulating proteins that enhance their tolerance to this stress.

Bacillus amyloliquefaciens alleviates the pathological injuries in mice infected with Schistosoma japonicum by modulating intestinal microbiome

Schistosoma japonicum causes serious pathological organ damage and alteration of the intestinal microbiome in the mammalian host, threatening the health of millions of people in China. Bacillus amyloliquefaciens has been reported to be able to alleviate the damage to the gut and liver and maintain the homeostasis of the intestinal microenvironment. However, it was unclear whether B. amyloliquefaciens could alleviate the hepatic and intestinal symptoms caused by S. japonicum. In this study, the intragastric administration of B. amyloliquefaciens was performed to treat S. japonicum-infected mice during the acute phase. Histopathological analysis and 16S rRNA gene sequencing were used to evaluate the pathological damage and changes in the intestinal microbiome. The results of the study showed that B. amyloliquefaciens treatment significantly reduced the degree of granuloma and fibrosis in infected mice. Additionally, recovery of diversity in the intestinal microbiome, decrease in the relative abundance of potential pathogenic bacteria such as Escherichia-Shigella, and reshaping of the interactive network between genera in the intestine were also observed after treatment with B. amyloliquefaciens. Our findings indicated that treatment with B. amyloliquefaciens effectively alleviated the pathological injuries of the liver and intestine in mice infected with S. japonicum by modulating the intestinal microbiome, implying that this probiotic can function as an effective therapeutic agent against schistosomiasis. We hope our study will provide auxiliary strategies and methods for the early prevention of schistosomiasis japonica.

Identification and functional analysis of non-coding regulatory small RNA FenSr3 in Bacillus amyloliquefaciens LPB-18

Bacillus amyloliquefaciens is an interesting microbe in the food processing and manufacturing industries. Non-coding small RNAs (sRNAs) have been shown to play a crucial role in the physiology and metabolism of bacteria by post-transcriptionally regulating gene expression. This study investigated the function of novel sRNA FenSr3 by constructing fenSr3 deficient strain and complementary strains in B. amyloliquefaciens LPB-18 , which were named LPN-18N and LPB-18P, respectively. The result showed significant differences in fengycin yield between strain LPB -18N and LPB-18P. The production of fengycin was significantly enhanced in B. amyloliquefaciens LPB-18N, compared with that of the strain LPB-18 from 190.908 mg/L to 327.598 mg/L. Moreover, the production of fengycin decreased from 190.464 mg/L to 38.6 mg/L in B . amyloliquefaciens LPB-18P. A comparative transcriptome sequencing was carried out to better understand the complex regulatory mechanism. Transcription analysis revealed that 1037 genes were differentially expressed between B. amyloliquefaciens LPB-18 and B. amyloliquefaciens LPB-18N, including the key regulatory genes in fatty acid, amino acid biosynthesis, and central carbon metabolism, which could provide sufficient quantities of building precursors for fengycin biosynthesis. The biofilm formation and sporulation was also enhanced in the strain LPB-18N, which indicates that FenSr3 could play a vital role in stress resistance and promotes survival in B. amyloliquefaciens. Some sRNAs involved in stress response have been identified in the literature, but their regulatory roles in fengycin production remain unclear. The study will contribute a novel perspective to the regulation mechanism of biosynthesis and the optimization of key metabolites of B. amyloliquefaciens.

A marine lipopeptides-producing Bacillus amyloliquefaciens HY2-1 with a broad-spectrum antifungal and antibacterial activity and its fermentation kinetics study

The antagonistic Bacillus amyloliquefaciens HY2-1 was a marine microbiology that was isolated previously from the seabed silt of Beibu Gulf in China by dual culture with Penicillium digitatum. As a continuous study, the present work focused on evaluating the antimicrobial activity, identifying the produced active components, and revealing the fermentation characteristics of B. amyloliquefaciens HY2-1, respectively. It was found that B. amyloliquefaciens HY2-1 exhibited a broad-spectrum antimicrobial activity against the tested seven phytopathogenic fungi and five pathogenic bacteria by producing Bacillus lipopeptides such as fengycin A (C₁₄ to C₁₉ homologues) and surfactin (C₁₄ and C₁₅ homologues). Morphological observation of P. digitatum under light microscope, scanning electron microscopy, transmission electron microscopy, and fluorescence microscope inferred that B. amyloliquefaciens exerted the antagonistic activity by damaging the fungal cell membrane, thus inhibiting the mycelium growth and sporification of phytopathogenic fungi. As a marine microbiology, our results showed that B. amyloliquefaciens could survive and metabolize even at the culture condition with 110 g/L of NaCl concentration, and the produced antimicrobial compounds exhibited excellent thermostability and acid-alkali tolerance. The dynamic models were further constructed to theoretically analyze the fermentation process of B. amyloliquefaciens HY2-1, suggesting that the synthesis of antimicrobial compounds was coupled with both cell growth and cell biomass. In conclusion, the marine lipopeptides-producing B. amyloliquefaciens HY2-1 showed a promising prospect to be explored as a biocontrol agent for plant disease control of crops and postharvest preservation of fruits and vegetables, especially due to its outstanding stress resistance and the broad-spectrum and effective antagonist on various phytopathogenic fungi.

Isolation of a potential probiotic strain Bacillus amyloliquefaciensLPB-18 and identification of antimicrobial compounds responsible for inhibition of food-borne pathogens

This study was carried out to screen a potential probiotic microbe with broad-spectrum antagonistic activity against food-borne pathogens and identify the antimicrobial compounds. Based on morphological and molecular analysis, a new Bacillus strain with the ability to produce effective antimicrobial agents was isolated from the breeding soil of earthworms and identified as having a close evolutionary footprint to Bacillus amyloliquefaciens. The antimicrobial substances produced by B. amyloliquefaciens show effective inhibition of Aspergillus flavus and Fusarium oxysporum in an agar diffusion assay. Antimicrobial agents were identified as a series of fengycin and its isoforms (fengycin A and fengycin B) after being submitted to RT-HPLC and MALDI-TOF MS analyses. To evaluate the probiotic activity of the B. amyloliquefaciens, antibiotic safety and viability of the isolated strain in a simulated gastrointestinal environment were carried out. The safety test result revealed that strain LPB-18 is susceptible to multiple common antibiotics. Moreover, acidic condition and bile salts assay were carried out, and the results revealed that it couble be a potential probiotic microbe B. amyloliquefaciens LPB-18 is good choice for biological strains in agricultural commodities and animal feedstuffs.

Improving acetoin production through construction of a genome-scale metabolic model

Acetoin was widely used in food, medicine, and other industries, because of its unique fragrance. Bacillus amyloliquefaciens was recognized as a safe strain and a promising acetoin producer in fermentation. However, due to the complexity of its metabolic network, it had not been fully utilized. Therefore, a genome-scale metabolic network model (iJYQ746) of B. amyloliquefaciens was constructed in this study, containing 746 genes, 1736 reactions, and 1611 metabolites. The results showed that Mg²⁺, Mn²⁺, and Fe²⁺ have inhibitory effects on acetoin. When the stirring speed was 400 rpm, the maximum titer was 49.8 g L^-1. Minimization of metabolic adjustments (MOMA) was used to identify potential metabolic modification targets 2-oxoglutarate aminotransferase (serC, EC 2.6.1.52) and glucose-6-phosphate isomerase (pgi, EC 5.3.1.9). These targets could effectively accumulate acetoin by increasing pyruvate content, and the acetoin synthesis rate was increased by 610% and 10%, respectively. This provides a theoretical basis for metabolic engineering to reasonably transform B. amyloliquefaciens and produce acetoin.

Research advances in probiotic fermentation of Chinese herbal medicines

Chinese herbal medicines (CHM) have been used to cure diseases for thousands of years. However, the bioactive ingredients of CHM are complex, and some CHM natural products cannot be directly absorbed by humans and animals. Moreover, the contents of most bioactive ingredients in CHM are low, and some natural products are toxic to humans and animals. Fermentation of CHM could enhance CHM bioactivities and decrease the potential toxicities. The compositions and functions of the microorganisms play essential roles in CHM fermentation, which can affect the fermentation metabolites and pharmaceutical activities of the final fermentation products. During CHM fermentation, probiotics not only increase the contents of bioactive natural products, but also are beneficial for the host gut microbiota and immune system. This review summarizes the advantages of fermentation of CHM using probiotics, fermentation techniques, probiotic strains, and future development for CHM fermentation. Cutting-edge microbiome and synthetic biology tools would harness microbial cell factories to produce large amounts of bioactive natural products derived from CHM with low-cost, which would help speed up modern CHM biomanufacturing.

Production of glutathione from probiotic Bacillus amyloliquefaciens KMH10 using banana peel extract

Glutathione, a tri-peptide (glutamate-cysteine-glycine) with the thiol group (-SH), is most efficient antioxidative agent in eukaryotic cells. The present study aimed to isolate an efficient probiotic bacterium having the potential to produce glutathione. The isolated strain Bacillus amyloliquefaciens KMH10 showed antioxidative activity (77.7 ± 2.56) and several other essential probiotic attributes. Banana peel, a waste of banana fruit, is chiefly composed of hemicellulose with various minerals and amino acids. A consortium of lignocellulolytic enzyme was used for the saccharifying banana peel to produce 65.71 g/L sugar to support the optimal glutathione production of 181 ± 4.56 mg/L; i.e., 1.6 folds higher than the control. So, the studied probiotic bacteria could be an effective resource for glutathione; therefore, the stain could be used as natural therapeutics for the prevention/treatment of different inflammation-related gastric ailments and as an effective producer of glutathione using valorized banana waste that has excellent industrial relevance.

Preparing Biosurfactant Glucolipids from Crude Sophorolipids via Chemical Modifications and Their Potential Application in the Food Industry

This investigation developed a novel strategy for efficiently preparing glucolipids (GLs) by chemically modifying crude sophorolipids. Running this strategy, crude sophorolipids were effectively transformed into GLs through deglycosylation and de-esterification, with a yield of 54.1%. The acquired GLs were then purified via stepwise extractions, and 66.2% of GLs with 95% purity was recovered. GLs are more hydrophobic and present a stronger surface activity than acidic sophorolipids (ASLs). More importantly, these GLs displayed a superior antimicrobial activity to that of ASLs against the tested Gram-positive food pathogens, with a minimum inhibitory concentration of 32-64 mg/L, except against E. coli . This activity of GLs is pH-dependent and especially more powerful under acidic conditions. The mechanism involved is possibly associated with the more efficient adsorption of GLs, as demonstrated by the hydrophobicity of the cell membrane. These GLs could be used as antimicrobial agents for food preservation and health in the food industry.

Investigating the effects of biodegradable microplastics and copper ions on probiotic (Bacillus amyloliquefaciens): Toxicity and application

Currently, microplastic pollution is more serious and complicates the toxic effects of other co-existing pollutants in the environment. However, the effect and mechanism of biodegradable plastics on the growth and metabolism of probiotic remain unclear. This work selected Bacillus amyloliquefaciens as model bacterium for a three-day exposure experiment to probe the issues. The results showed that 100 mg/L polylactic acid microplastics (PLA MPs) (3-4 mm, flake shape) caused oxidative damage to cell membranes, disrupted cell wall composition and inhibited cell growth by 21.2-27.5 %. The toxicity was not simply additive or synergistic effects when PLA MPs (100 mg/L) and copper ions (10 mg/L) coexisted. PLA MPs did not significantly increase the toxicity of copper to bacteria, instead triggered some mechanisms to resist the toxicity of copper. The bacteria formed spores to resist PLA MPs, while the copper ions toxicity was weaken by chelation and efflux. It is worth noting that copper ions instead increased the expression of genes related fengycin and iturin then improving the bacteriostatic activity of the probiotic. This paper deeply analyzes the toxicity mechanism of combined pollution on Bacillus amyloliquefacien, and also provides new perspective for helping to inhibit pathogenic bacteria under biodegradable microplastics and metal stress.

Effects of cranberry powder on the diversity of microbial communities and quality characteristics of fermented sausage

Fermented sausage is popular with many consumers because of its distinctive flavor, but the safety of it has attracted widespread attention. At present, nitrite is widely used in fermented meat products because of its ideal color and bacteriostatic effect, but nitrite can be transformed into nitrosamines, which cause strong carcinogenic effects. Therefore, it is urgent to actively explore safe and efficient nitrite substitutes. In this study, cranberry powder was selected as a natural substitute for nitrite during the production of fermented sausage due to its unique antioxidant and bacteriostatic properties. The results showed that adding an appropriate amount of cranberry powder (5 g/kg) promoted a better color of the fermented sausage and promoted the accumulation of aromatic compounds. Furthermore, Pediococcus and Staphylococcus became the dominant species, accounting for more than 90% in all samples. According to the Pearson correlation analysis, Staphylococcus and Pediococcus had positive effects on the quality characteristics of fermented sausage products. This study provided the latest information on the application of cranberry powder as a natural substitute for nitrite in the process of manufacturing fermented sausage, and it also introduced an advanced solution to improve the quality characteristics and safety of fermented sausage products during processing.

Autoclaved Diet with Inactivated Spores of Bacillus spp. Decreased Reproductive Performance of Muc2−/− and Muc2+/− Mice

Simple Summary

Within barrier facilities for the housing of laboratory animals, the sterilization of feed, bedding, and cages is used to reduce contact with bacteria. However, in nature, animals come into contact with a lot of bacteria. We investigated the effect of an autoclaved diet on the reproductive performance of Muc2^−/− mice. Muc2^−/− mice develop intestinal barrier defects and are sensitive to changes of the gut microbiota. We have shown that the autoclaved diet negatively affects the reproductive performance of Muc2^−/− females and their healthy Muc2^+/− siblings. Thus, the autoclaved diet led to earlier rectal prolapse of Muc2^−/− females combined with intestinal inflammation, compared to mice fed with the non-autoclaved diet. We hypothesize that this effect is due to the reduction of the diet nutritional value and inactivation of Bacillus spp. spores in the autoclaved diet.

Abstract

Within barrier facilities, autoclaved diet and bedding are used for husbandry of laboratory rodents. Bacillus spp. are ubiquitous in nature and some of them are known as probiotics. Inactivation of the Bacillus spores and reduction of the diet nutritional value due to autoclavation could be especially critical for immunodeficient mice. We studied the effect of the autoclaved and non-autoclaved diets on the reproductive performance and the age of prolapse manifestation in Muc2^−/− mice with impaired gut barrier function and, therefore, sensitive to change of microbiota. We found that the non-autoclaved diet led to enhancement of the fertility index of Muc2^−/− and Muc2^+/− female mice. The non-autoclaved diet affected the prolapse of Muc2^−/− mice that occurred later in comparison with females eating the autoclaved diet. We showed that Bacillus spp. was present in the non-autoclaved diet and feces of mice on the non-autoclaved diet. Bacterial strains of the non-autoclaved diet and feces belonged to B. amyloliquefaciens, B. thuringiensis, B. subtilis, Lysinibacillus macrolides, B. cereus, and other representatives of Bacillus spp. Moreover, autoclavation of the diet affected on the percent of the blood and spleen immune cells, the bacterial composition of the intestine, and increased the level of methionine in the thigh muscle of mice. Enhanced reproductive performance and delayed prolapse manifestation in Muc2^−/− mice could be due to improved digestion, as Bacillus spp. from diet and feces had enzymatic activity.

Exopolysaccharides of Bacillus amyloliquefaciens Amy-1 Mitigate Inflammation by Inhibiting ERK1/2 and NF-κB Pathways and Activating p38/Nrf2 Pathway

Bacillus amyloliquefaciens is a probiotic for animals. Evidence suggests that diets supplemented with B. amyloliquefaciens can reduce inflammation; however, the underlying mechanism is unclear and requires further exploration. The exopolysaccharides of B. amyloliquefaciens amy-1 displayed hypoglycemic activity previously, suggesting that they are bioactive molecules. In addition, they counteracted the effect of lipopolysaccharide (LPS) on inducing cellular insulin resistance in exploratory tests. Therefore, this study aimed to explore the anti-inflammatory effect and molecular mechanisms of the exopolysaccharide preparation of amy-1 (EPS). Consequently, EPS reduced the expression of proinflammatory factors, the phagocytic activity and oxidative stress of LPS-stimulated THP-1 cells. In animal tests, EPS effectively ameliorated ear inflammation of mice. These data suggested that EPS possess anti-inflammatory activity. A mechanism study revealed that EPS inhibited the nuclear factor-κB pathway, activated the mitogen-activated protein kinase (MAPK) p38, and prohibited the extracellular signal-regulated kinase 1/2, but had no effect on the c-Jun-N-terminal kinase 2 (JNK). EPS also activated the anti-oxidative nuclear factor erythroid 2–related factor 2 (Nrf2) pathway. Evidence suggested that p38, but not JNK, was involved in activating the Nrf2 pathway. Together, these mechanisms reduced the severity of inflammation. These findings support the proposal that exopolysaccharides may play important roles in the anti-inflammatory functions of probiotics.

Extraction and characterization of cyclic lipopeptides with antifungal and antioxidant activities from Bacillus amyloliquefaciens

AIMS

This study aimed to isolate active substances from metabolites of Bacillus amyloliquefaciens SJ100001 and examine their antifungal activity against Fusarium oxysporum (F. oxysporum) SJ300024 screened from the root-soil of cucumber wilt.

METHODS AND RESULTS

An active substance, anti-SJ300024, was obtained from the fermentation broth of strain SJ100001 by reversed-phase silica gel and gel chromatography, and further got its chemical structure as cyclic lipopeptide Epichlicin through nuclear magnetic resonance (NMR) and mass spectrometry (MS). In vitro experiments showed that Epichlicin had a better inhibitory rate (67.46%) against the strain SJ300024 than the commercially available fungicide hymexazol (45.1%) at the same concentration. The MTT assays proved that Epichlicin was non-cytotoxic, besides it also had good free radical scavenging ability and total reducing ability.

CONCLUSIONS

Epichlicin isolated from strain SJ100001 can effectively control F. oxysporum SJ300024 screened from the root-soil of cucumber wilt.

SIGNIFICANCE AND IMPACT OF THE STUDY

Epichlicin may be used as an environmentally friendly and efficient biocontrol agent for controlling Fusarium wilt of cucumber and reducing crop losses. More importantly, the non-cytotoxicity of Epichlicin can avoid harm to consumers. Additionally, Epichlicin has broad application prospects in medicine due to its antioxidant properties.

Bioactivities evaluation of an endophytic bacterial strain Bacillus velezensis JRX-YG39 inhabiting wild grape

BACKGROUND

Botrytis cinerea can cause serious disease on lots of plant hosts during growth and postharvest storage. Biocontrol is known to be eco-friendly methods to control pathogens. Plant endophytic bacteria are generally considered as beneficial organisms, since they can promote plant growth and enhance plant immune system. Thus, screening biological control agents is very important for sustainable plant protection.

RESULTS

Fifty-six endophytic bacteria were obtained from wild grape. Sixteen isolates and their extracts exhibited significant antifungal activity against B. cinerea. Particularly, strain JRX-YG39 with the strongest inhibition ability had a broad-spectrum antifungal activity. Combining 16S rDNA analysis and the phylogenetic results based on gyrA and gyrB genes, JRX-YG39 was assigned as Bacillus velezensis. JRX-YG39 could produce bioactive VOCs and obviously depressed mycelia growth of B. cinerea. It was confirmed that VOCs released by JRX-YG39 could significantly promote growth and induce defense of Arabidopsis thaliana. Thirty-one bioactive secondary metabolites were further identified from JRX-YG39 culture by gas chromatography-mass spectrometry analysis. Dibutyl phthalate, a potential antifungal substance, was the major compound accounting for 78.65%.

CONCLUSIONS

B. velezensis JRX-YG39 has wide broad-spectrum antagonistic activity and significant plant promotion activity. Hence, B. velezensis JRX-YG39 will provide a valuable constituent of modern agricultural practice as biofertilizers and biocontrol agents.

Biocontrol Ability of the Bacillus amyloliquefaciens Group, B. amyloliquefaciens, B. velezensis, B. nakamurai, and B. siamensis, for the Management of Fungal Postharvest Diseases: A Review

The Bacillus amyloliquefaciens group, composed of B. amyloliquefaciens, B. velezensis, B. nakamurai, and B. siamensis, has recently emerged as an interesting source of biocontrol agents for the management of pathogenic fungi. In this review, all the reports regarding the ability of these species to control postharvest fungal diseases have been covered for the first time. B. amyloliquefaciens species showed various antifungal mechanisms, including production of antifungal lipopeptides and volatile organic compounds, competition for nutrients, and induction of disease resistance. Most reports discussed their use for the control of fruit diseases. Several strains were studied in combination with additives, improving their inhibitory efficacies. In addition, a few strains have been commercialized. Overall, studies showed that B. amyloliquefaciens species are a suitable environmentally friendly alternative for the control of postharvest diseases. However, there are still crucial knowledge gaps to improve their efficacy and host range.