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PubMed2025

Mutation of the gidB gene causes intrinsic streptomycin resistance in Bacillus velezensis.

Bacillus velezensis strain DMB07, isolated from the traditional fermented Korean soybean meju, exhibits resistance to streptomycin [minimum inhibitory concentration (MIC) 128 mg/L]. To shed light on the genetic background behind this phenotype, this study determined the complete genome sequence of strain DMB07 and compared it with the genomes of two B. velezensis strains that are sensitive to streptomycin. Compared with the streptomycin-sensitive strains, in strain DMB07 there was a mutation of a nucleotide (C58T) of the 16 S rRNA (guanine527-N7)-methyltransferase gene (gidB) that leads to a change in the amino acid sequence of the protein (Arg20Cys). This sequence of gidB gene was previously linked with streptomycin resistance. To test the hypothesis that this change in the gidB gene sequence of strain DMB07 confers streptomycin resistance, a temperature-sensitive plasmid, pIMAY-tgidBT58C, was constructed for site-directed mutation (from thymine to cytosine) of nucleotide 58 of gidB in strain DMB07. The resulting strain, DMB07gidBT58C, showed the decreased MIC value (32 mg/L) against streptomycin. Furthermore, introduction of the wild-type gidB gene into strain DMB07gidBT58C resulted in recovery of the MIC for streptomycin to 128 mg/L. Thus, a single mutation of the nucleotide sequence of the gidB gene can confer resistance to streptomycin.

Streptomycin↗
PubMed2026

Biocontrol Potential of a Novel Bacillus velezensis Strain Against Major Soft Rot Bacteria Pectobacterium and Dickeya.

Management of soft rot Pectobacteriaceae (SRP) remains a major challenge because effective control options such as bactericides, chemical treatments, or resistant commercial varieties are currently lacking. In a quest for an effective control measure against SRP, we isolated bacteria from soil and potato samples from potato fields across Montana. The bacterial isolates were screened for their effective suppression of major soft rot and blackleg pathogens Pectobacterium brasiliense strain Pb1692 and Dickeya dianthicola strain ME23. We screened more than 3,000 bacterial isolates using inhibition-zone assays on nutrient agar plates. From this collection, we identified a strong antagonist effective against Pb1692 and ME23. This isolate successfully suppressed potato soft rot and blackleg disease in both laboratory and greenhouse evaluations. Genome sequencing identified the bacterial antagonist as Bacillus velezensis strain DN539, which can survive well at 8°C, a potato postharvest storage temperature. We enriched the B. velezensis DN539 supernatant in bioactive fractions, and mass spectrometry analysis identified the bioactive compound as isomers of surfactin. Scanning electron microscopy identified that surfactin-enriched fraction resulted in the leakage of the cellular content of phytobacteria tested in our study in as little as 10 min, followed by complete degradation of bacterial cells within 1 h. The surfactin-enriched fraction also had antimicrobial effects against other economically important phytobacteria such as Erwinia amylovora, Xanthomonas campestris, and Pseudomonas syringae. These indicate that surfactin synthesized by Bacillus velezensis DN539 has potential to be developed as a biocontrol agent against broad range of phytobacteria.

Pectobacterium↗
PubMed2026

Integrated assessment of biocontrol potential and genome analysis of endophytic Bacillus velezensis MGL-B1 against mango stem-end rot.

Mango stem-end rot is a globally significant postharvest disease that severely threatens the mango industry, primarily caused by Botryosphaeria dothidea. However, information on biocontrol agents targeting this pathogen in mango remains limited. In this study, we isolated and identified a strain of Bacillus velezensis MGL-B1 from mango leaf tissues for the first time, which exhibited broad-spectrum antifungal activity. Both in vitro and in vivo assays demonstrated that MGL-B1 effectively inhibited the growth of B. dothidea, with an in vivo biocontrol efficacy reaching 83.72 ± 5.10%, comparable to that of the commonly used chemical fungicide thiabendazole. Further mechanistic analysis revealed that MGL-B1 acts by directly disrupting the integrity of the pathogen's mycelial cell membrane. In addition, its released volatile organic compounds (VOCs) also displayed significant antifungal activity, with components such as 2-nonanone, 2-nonanol, and phenylethyl alcohol being confirmed to exert antifungal effects in in vitro fumigation assays. qPCR analysis showed that MGL-B1 treatment significantly upregulated the transcriptional levels of genes involved in plant-pathogen interaction, phenylpropanoid biosynthesis, and antioxidant defense pathways in mango fruits, with upregulation folds of 16.32, 37.19, and 75.93, respectively; meanwhile, the expression of browning-related genes such as polyphenol oxidase (PPO) was markedly suppressed. Whole-genome sequencing further revealed 14 biosynthetic gene clusters for antimicrobial compounds, including five unknown gene clusters. Collectively, B. velezensis MGL-B1 represents a promising biocandidate strain with multiple antifungal mechanisms and excellent control efficacy, providing a valuable resource for green and sustainable management of mango diseases.

Mangifera↗
PubMed2026

Mulberry-derived endophytic Bacillus velezensis suppresses gray mold and promotes mulberry growth via reshaping the root metabolism and microbiome.

INTRODUCTION: Gray mold is an important fungal disease caused by Botrytis cinerea which threatens global agriculture. As chemical control faces limitations, biological control using Bacillus has gained attention for its environmental friendliness and growth promotion. However, their ecological basis and application potential in mulberry gray mold control remain insufficiently understood. OBJECTIVE: This study aimed to evaluate the biocontrol efficacy of the mulberry derived endophytic strain Bacillus velezensis ZJU_268 and to investigate its associated effects on plant growth, root-associated microbiomes, and metabolic profiles. METHODS: Greenhouse assays were combined with genomic and comparative genomic analyses, amplicon sequencing, non-targeted metabolomics, and functional validation of isolated microbes and metabolites to assess the effects of ZJU_268 and its cell free supernatant (CFS) on mulberry seedlings. RESULTS: This study isolated a mulberry derived endophytic bacterium, B. velezensis ZJU_268, which exhibits strong antifungal activity and reduces the incidence of gray mold in mulberry seedlings. Whole-genome sequencing and comparative genomic analyses revealed strain-specific regions and genes associated with root colonization, stress adaptation, and antimicrobial biosynthesis. Both live cells and CFS significantly promoted seed germination, seedling growth, and biomass accumulation in a dose dependent manner. Amplicon sequencing showed that ZJU_268 and its supernatant reshaped the mulberry root microbiome, enriching beneficial bacterial and fungal taxa while reducing potentially pathogenic members. Cultivable members of the enriched microbiota displayed strong antifungal activity against B. cinerea and promoted mulberry growth. Metabolomic profiling further showed that ZJU_268 and its supernatant were associated with marked metabolic shifts in mulberry roots, accompanied by the accumulation of selected metabolites that supported the growth of representative enriched isolates. CONCLUSIONS: This study demonstrates that ZJU_268 suppresses gray mold and promotes mulberry growth in association with direct antagonistic activity, microbiome restructuring, and holobiont-level metabolic shifts, providing a promising biological strategy for sustainable mulberry disease management.

Bacillusvelezensis↗
PubMed2005

Bacillus velezensis sp. nov., a surfactant-producing bacterium isolated from the river Vélez in Málaga, southern Spain.

Two Gram-positive, endospore-forming bacterial strains, CR-502T and CR-14b, which produce surfactant molecules are described. Phenotypic tests and phylogenetic analyses showed these strains to be members of the genus Bacillus and related to the species Bacillus atrophaeus, Bacillus mojavensis, Bacillus subtilis, Bacillus vallismortis and Bacillus amyloliquefaciens, although they differ from these species in a number of phenotypic characteristics. DNA-DNA hybridization confirmed that they show less than 20 % hybridization with the above-mentioned species and therefore represent a novel species of Bacillus. The DNA G+C content is 46.4 mol% in strain CR-502T and 46.1 mol% in strain CR-14b. The main fatty acids in strain CR-502T are 15 : 0 anteiso (32.70 %), 15 : 0 iso (29.86 %) and 16 : 0 (13.41 %). The main quinone in strain CR-502T is MK-7 (96.6 %). In the light of the polyphasic evidence gathered in this study, it is proposed that these strains be classified as a novel species of the genus Bacillus, with the name Bacillus velezensis sp. nov. The type strain (CR-502T=CECT 5686T=LMG 22478T) was isolated from a brackish water sample taken from the river Vélez at Torredelmar in Málaga, southern Spain.

Bacillus↗
PubMed2026

Biocontrol Potential and Mechanism of Endophytic Bacillus velezensis WSR1 Against Rubber Tree Anthracnose.

Fungal leaf anthracnose, caused by Colletotrichum species, is a major leaf disease of rubber trees, significantly reducing global natural rubber yields. To explore sustainable and safe biological control strategies, eight bacterial strains were isolated from rubber tree tissues, demonstrating antagonistic activity against Colletotrichum pathogens (C. siamense and C. australisinense). Among these, WSR1 exhibited the most pronounced antifungal effect, with inhibition rates of 87.64 and 89.03% against C. siamense and C. australisinense, respectively. Genomic analysis identified WSR1 as Bacillus velezensis. In pot experiments, WSR1 exhibited preventive efficacy of 77.24 and 73.42% for C. siamense- and C. australisinense-induced anthracnose, respectively, with therapeutic efficacy of 42.28 and 45.57%. WSR1 compromised the integrity of the cell walls and membranes of both C. siamense and C. australisinense, while inducing reactive oxygen species accumulation within the hyphae. Additionally, WSR1 enhanced rubber tree resistance to anthracnose by activating defense-related enzymes, including phenylalanine ammonia-lyase, polyphenol oxidase, and peroxidase. Plate assays and genomic analysis revealed that WSR1 secretes fungal cell wall-degrading enzymes (cellulases, pectinases, and proteases) and siderophores. Furthermore, liquid chromatography-mass spectrometry and gene cluster analysis confirmed the synthesis of antagonistic secondary metabolites, such as surfactin, macrolactin H, and fengycin. This study represents the first identification of B. velezensis as a potential biocontrol agent against rubber tree anthracnose, offering a promising candidate for the eco-friendly management of rubber tree diseases.

C. australisinense↗
PubMed2026

Intestinal organoid screen reveals that Bacillus velezensis PGM541 promotes epithelial proliferation via its metabolite butyric acid.

BACKGROUND: Probiotics have been widely used for the regulation of intestinal health. Current screening methods for probiotics typically rely on animal or two-dimensional cell models. In this study, we employed intestinal organoids to identify a candidate probiotic strain. Furthermore, we investigated the potential mechanisms through which this strain and its active metabolites exert their effects, thereby evaluating the efficacy of this screening approach. RESULTS: Firstly, candidate probiotic strain PGM541 was identified from a porcine-derived Bacillus library by assessing organoid viability. Subsequently, to validate the organoid screening reliability, the potential mechanism of strain PGM541 on the intestinal epithelium was investigated; it was found to exhibit probiotic functions by regulating cell proliferation in both in vitro organoid and in vivo piglet models. Furthermore, organoid screening combined with metabolomic analysis identified butyric acid (BA) as the key bioactive metabolite responsible for driving epithelial proliferation. Whole-genome and transcriptomic analyses revealed the biosynthetic pathway of BA in strain PGM541. Importantly, BA receptor blockade experiments directly confirmed that BA enhances epithelial proliferation via interaction with the FFAR2 receptor, thereby validating its functional activity. Additionally, strain PGM541 exhibited protective effects against dextran sulfate sodium (DSS)-induced colitis, further validating the effectiveness of the intestinal organoid platform for probiotic screening. CONCLUSIONS: The probiotic strain PGM541, which was screened using intestinal organoids, promotes intestinal epithelial cell proliferation via its metabolite BA activating the FFAR2 receptor. These findings demonstrate that the intestinal organoid model serves as an effective platform for both preliminary probiotic screening and mechanistic investigation. Video Abstract.

Animals↗
PubMed2026

Revealing Functional Traits of Insect Pest Suppressive Rhizobacterial Strains Through Comparative Genomics.

Root inoculation with rhizobacteria is an emerging strategy to enhance plant resistance to aphid herbivory, yet the microbial functional traits underpinning these responses remain poorly characterised. Here, we present a comparative genomic analysis of five rhizobacteria (Acidovorax radicis N35, Bacillus subtilis B171, Bacillus velezensis FZB42, Rhizobium radiobacter F4 and Pseudomonas simiae WCS417r) that suppress aphids when inoculated onto barley. As expected, functional variation largely reflected phylogenetic relatedness; however, candidate traits implicated in modulation of plant immune defences were conserved across all strains, including biosynthesis of 2,3-butanediol, riboflavin and salicylic acid. Additional shared functions, linked to plant defence signalling, included phytoene and squalene biosynthesis (absent in P. simiae) and N-acyl homoserine lactone quorum sensing (absent in Bacillus spp.). Strain-specific traits were also identified, including surfactin production in Bacillus spp. and hydrogen cyanide biosynthesis in A. radicis and P. simiae. Comparison with a broader collection of rhizobacteria revealed that many putative plant-beneficial functions identified were widely conserved, including among closely related phytopathogens. This extensive functional overlap suggests aphid suppression cannot be explained solely by presence or absence of broad functional traits, but rather by specific trait combinations, regulatory differences, or context-dependent expression. This highlights the need for genome-informed approaches for bioinoculant discovery.

Animals↗
PubMed2026

Evaluation of Indigenous Bacillus Strains from Asian Fermented Foods for Probiotic Properties.

Bacillus species hold particular importance due to their versatile enzymatic repertoire and ability to synthesize diverse bioactive metabolites. In this study, two fermented food-derived strains, Bacillus siamensis BB3 (from douchi) and Bacillus velezensis TMA10 (from tapai) were evaluated for their probiotic, anti-microbial and functional potentials. Both strains exhibited desirable probiotic characteristics, including desirable tolerance to simulated gastric and intestinal conditions, with BB3 showing greater acid tolerance than TMA10. Safety assessments confirmed the absence of hemolytic activity, virulence factors and antibiotic resistance genes. Whole genome sequencing showed that the strains harbored genomic sequences for a wide range of metabolites, including non-ribosomal peptides and polyketides. Ethyl acetate (EtOAc) extracts from both strains demonstrated broad-spectrum anti-microbial activity against several indicator microorganisms, including Listeria grayi, Bacillus cereus, Serratia marcescens, Escherichia coli, and Pseudomonas aeruginosa, with TMA10 additionally inhibiting MRSA and Streptococcus mutans. Liquid Chromatography-Mass Spectrometry profiling identified key anti-microbial compounds, namely surfactins, macrolactins, bacillaene from BB3 and TMA10. In addition, difficidins were also detected from TMA10. Genomic analysis further indicated diverse carbohydrate utilization capacities; both strains encoded pathways for sucrose, raffinose-family oligosaccharides and lactose metabolism, while TMA10 possessed pathways for trehalose, glucomannan and arabinoxylan degradation. Both strains also showed anti-oxidant activity, with enhanced effects observed in their cell-free supernatants and heat-killed preparations. Overall, these findings highlight BB3 and TMA10 as promising candidates for the development of fermented food-derived Bacillus probiotics and functional cultures with anti-microbial, anti-oxidant, and broad carbohydrate-utilization capabilities.

Bacillus↗
PubMed2025

Broad-spectrum antibacterial and antibiofilm activity of dandelion endophytic bacteria against multidrug-resistant bacteria.

Microbial secondary metabolites have long served as a key source of natural product-based drugs. This study evaluates the antibacterial, antibiofilm, and antioxidant activities of endophytic bacteria derived from dandelion, focusing on their effects against multidrug-resistant (MDR) clinical isolates. In total, 33 endophytic bacteria strains were isolated from Taraxacum ohwianum, representing 15 genera. Among these, 13 exhibited antibacterial activity, with 6 demonstrating efficacy against MDR clinical isolates. The endogenous strain Bacillus velezensis DR8 showed strong antibacterial activity against all three MDR strains tested and exerted inhibitory effects on the biofilm formation and dispersal of methicillin-resistant Staphylococcus aureus. Genome sequencing and antibiotics and secondary metabolite analysis shell analysis revealed that this strain harbors 12 biosynthetic gene clusters (BGCs) associated with secondary metabolite production. Of these, seven BGCs exhibited ≥ 80% similarity to known clusters, suggesting the potential to synthesize surfactin, difficidin, fengycin, bacillaene, macrolactin H, bacilysin, and bacillibactin. Overall, these findings indicate that endophytic bacteria from dandelion are a potential source of antibacterial compounds and biofilm formation inhibitors.

Endophytes↗
PubMed2025

Single-Cell Force Spectroscopy Uncovers Root Zone- and Bacteria-Specific Interactions.

Understanding root-bacteria interactions with plant growth-promoting rhizobacteria (PGPR) is key to developing effective biofertilizers for sustainable agriculture. We performed single-cell force spectroscopy using the atomic force microscope (AFM) to study the primary attachment of two PGPR, Bacillus velezensis and Pseudomonas defensor, to different regions of Arabidopsis thaliana roots. Force measurements with individual cells uncovered distinct attachment strategies by each strain, involving binding via micrometer-long polymers from both bacteria and root surfaces. Flagella differentially affected the binding interactions of each PGPR; their removal altered binding characteristics differently for each strain, highlighting the importance of flagella in early root colonization. Using silica beads to mimic the negatively charged bacteria, we demonstrated the influence of electrostatic forces on root-bacteria interactions. We also examined interactions with abiotic surfaces of varying surface energies, revealing the roles of hydrophilic and hydrophobic forces in initial binding. Our measurements show that differences in the physicochemical properties of bacteria and roots are responsible for variations in primary attachment strategies between PGPR strains and root regions. Parallel fluorescence measurements corroborated our AFM single-cell analysis. Overall, our results provide a nanoscale view of bacterial attachment to roots, offering key insights into how beneficial bacteria colonize roots, crucial for enhancing biofertilizer effectiveness.

Plant Roots↗
PubMed2026

The Mediating Role of Immune Cells in the Genetically Predicted Relationship between Gut Microbiota and Puerperal Sepsis: A Mendelian Randomization Study.

INTRODUCTION: The causal relationship between gut microbiota and puerperal sepsis (PS) remains unclear, and there is a lack of in-depth research regarding the potential mediating role of immune cells in this context. OBJECTIVE: This study aims to investigate the causal relationship between gut microbiota and PS using Mendelian randomization (MR) analysis and to assess the mediating effects of immune cells on the risk of PS onset through mediation analysis. MATERIALS AND METHODS: We selected data from large-scale genome-wide association studies (GWAS) involving 473 gut microbiota species, 731 immune cell phenotypes, and PS datasets. Univariate MR (UVMR) analysis was employed to explore the causal relationship between gut microbiota and PS, with the primary statistical method being inverse variance weighting (IVW). Multiple statistical models were applied for sensitivity analysis to minimize the confounding effects of horizontal pleiotropy and heterogeneity. Subsequently, a two-step mediation MR analysis was conducted to evaluate whether immune cells mediate the relationship between gut microbiota and PS. RESULTS AND DISCUSSION: Analysis using various statistical models indicated that 11 gut microbiota species (e.g., Azorhizobium, Bacillus velezensis, CAG-245 sp000435175, Lentimicrobiaceae, and Providencia) exhibited a causal relationship with PS. Further reverse causal analysis between PS and gut microbiota ruled out the possibility of reverse causality. The two-step mediation MR analysis demonstrated that the percentage of IgD-CD27- B cells (10.26%) and CD62L- monocytes (17.29%) partially mediated the effect of CAG-245 sp000435175 on PS risk. CONCLUSION: This study provides evidence of a causal relationship between the abundance of certain gut microbiota species and PS, while also revealing a potential mediating role of immune cells. These findings offer valuable theoretical insights into personalized treatment strategies and the development of novel diagnostic biomarkers for PS.

Humans↗
PubMed2026

Genomic and biosynthetic landscape of high-temperature Daqu microbiome.

As the core starter for Chinese Baijiu, high-temperature Daqu is produced through open solid-state fermentation with recurrent inoculation by mature Daqu, forming a rich yet largely untapped reservoir of genomes and bioactive compounds. This study constructs the High-temperature Daqu Fermentation Microbiome catalog using 463 metagenomes spanning the full fermentation cycle. The catalog comprises 4,264 metagenome-assembled genomes that are dereplicated into 252 representative genome-based species, 82 % of which are absent from current global food microbiome databases. It further contains 14.3 million non-redundant genes, of which 17.3 % are novel, and 17,031 biosynthetic gene clusters, of which 62.63 % are novel, thereby substantially expanding the known genomic and biosynthetic space of food microbiomes. Genome-resolved analyses revealed a U-shaped ecological trajectory, shifting from early Bacillus velezensis-enriched assemblages to transient dominance of lactic acid bacteria during peak thermogenesis, before returning in late fermentation to thermotolerant, spore-forming Bacillota and Actinomycetota. In parallel, biosynthetic potential was further organized into four recurrent, stage-enriched profiles, from RiPP-rich thermogenic states to mature-state assemblages enriched in PKS-, NRPS-, and terpene-related capacities, with Bacillus, Kroppenstedtia, and Saccharopolyspora constituting the principal biosynthetic reservoir. Together, this work uncovers a largely unexplored genomic and biosynthetic reservoir in high-temperature Daqu fermentation, providing a target resource for mining thermotolerant industrial enzymes, flavor-related genes, and bioactive metabolites with biotechnological potential.

Microbiota↗
PubMed2026

Draft genome sequences of three Bacillus spp. from the University of the Philippines Culture Collection.

This study reports the assembled and annotated draft genomes of three Bacillus spp. isolates from the University of the Philippines Culture Collection. Genome analysis predicted genes for stress tolerance, plant-growth promotion, and secondary metabolite production, highlighting their potential for diverse biotechnological applications in agriculture and natural product synthesis.

Bacillus↗