Search Results (1,797)

The rising global food demand requires boosting agricultural productivity without compromising environmental sustainability, especially in the face of intensive agrochemical use and soil degradation. Based on this, strain TRQ67 was isolated from wheat rhizosphere soil in the Yaqui Valley, Mexico, and characterized morphologically, biochemically, and genomically. Strain TRQ67 possesses a genome of 4.04 Mbp across 37 contigs with a G + C content of 46.3%, comprising 4127 coding DNA sequences (CDSs), and was identified as Bacillus velezensis through Overall Genome Relatedness Indices (OGRIs), including Average Nucleotide Identity (OrthoANI = 99.12%) and Genome-to-Genome Distance Calculator (Formula 2: 92.6%). The genome revealed key functional genes associated with auxin biosynthesis (trpABCDEF and yhcX), iron acquisition (dhbABF), nutrient solubilization (gabD, acnAB and pyc), stress response (clpCEPX and pspA), antifungal metabolite synthesis (srfAABCD, fenABCD and bmyABC), chemotaxis and motility (cheABCD, motAB, flgBCDEF, swrC), bacterial fitness (acoABR, acuABC and budABC), exopolysaccharide production (epsDEFHI), sporulation (spo0ABEF) and bioremediation. Predicted gene functions were supported by in vitro phenotypic assays; strain TRQ67 was able to solubilize phosphate (Solubilization Index of 4.1 ± 0.46), biosynthesize siderophores (Production Index of 1.70 ± 0.16), and produce indoles (6.52 ± 0.63 µg mL⁻¹). Furthermore, this strain demonstrated antagonistic activity against phytopathogenic fungi Fusarium languescens and Bipolaris sorokiniana, resulting in reductions in fungal growth area of 87.33% and 89.28%, respectively. These antagonistic effects are consistent with the presence of Biosynthetic Gene Clusters (BGCs) encoding lipopeptides (surfactin and fengycin), polyketides (difficidin, bacillaene and macrolactin H), dipeptides (bacilysin) and siderophores (bacillibactin), as identified through antiSMASH analysis. Finally, the strain significantly improved root (27.63%) and shoot (5.82%) biomass in wheat plants under controlled conditions. These results highlight Bacillus velezensis TRQ67 as a promising microbial inoculant with plant growth promotion capabilities and potential antifungal activity against phytopathogenic fungi, as evidenced by strong in vitro antagonistic activity, supporting its further evaluation for sustainable agricultural practices. Full article

Farnesol is a small isoprenoid metabolite that has emerged as a key regulator of fungal biology beyond its original identification as a quorum-sensing molecule in Candida albicans. This review examines farnesol across pathogenic and non-pathogenic fungi, emphasizing its roles in morphogenesis, biofilm development, stress adaptation, membrane-associated physiology, and ecological interaction. In pathogenic fungi, farnesol modulates virulence-related traits, antifungal susceptibility, and host interaction, while in non-pathogenic systems, it influences growth, differentiation, and metabolic balance. Evidence from Saccharomyces cerevisiae, Trichoderma, Candidozyma auris (formerly known as Candida auris), and other fungi highlights the context-dependent nature of its effects. We also discuss farnesol biosynthesis, secretion, and the apparent absence of canonical salvage pathways in fungi. Together, these findings support a broader view of farnesol as a multifunctional fungal metabolite that links signaling with metabolism. Understanding its diverse biological roles may clarify fungal evolution and inform future strategies targeting fungal persistence, adaptation, and antifungal tolerance. Full article

Chronic diseases and aging-related disorders are driven by interconnected mechanisms, including oxidative stress, low-grade inflammation, metabolic dysregulation, and glycation. Targeting these overlapping pathways remains a major challenge for conventional single-target therapeutics. In this context, endophytic fungi have emerged as a promising source of bioactive metabolites with multi-target pharmacological potential. This review provides a mechanistic overview of endophyte-derived metabolites, including alkaloids, terpenoids, polyketides, and phenolic compounds, with a focus on their ability to modulate key signaling pathways such as NF-κB, Nrf2, PI3K/Akt, AMPK, and the AGE–RAGE axis. Evidence from experimental studies suggests that these metabolites exhibit anticancer, anti-inflammatory, antioxidant, and metabolic regulatory effects through coordinated modulation of cellular signaling networks. Several endophyte-derived metabolites also possess antimicrobial activity against bacterial and fungal pathogens and may represent a promising source of novel anti-infective agents. Their ability to modulate host immune responses and microbial-associated signaling pathways further highlights their relevance for antimicrobial discovery and microbiome-based therapeutic strategies. Particular attention is given to pathway-level convergence in chronic diseases, including cancer, diabetes, and inflammation-associated disorders, as well as their relevance to aging and health span. The pharmacological potential of these compounds is discussed alongside key limitations, including issues related to bioavailability, reproducibility, and translation into clinical applications. Overall, endophytic fungal metabolites represent a structurally diverse and mechanistically rich resource for the development of multi-target therapeutic strategies. Future integration of metabolomics, genome mining, and advanced disease models will be essential to bridge the gap between experimental findings and clinical application. Full article

Microbial fertilizers may improve phosphorus availability and pH in acidic soils, but field evidence linking these changes with medicinal plant biomass and specialised metabolite accumulation remains limited. Here, a one-season field experiment was conducted in acidic yellow soil in Guizhou Province, China, using four fertilization regimes for Lonicera macranthoides: an organic fertilizer plus compound fertilizer control (CK), a bacterial consortium (T1), a simplified bacterial combination (T2), and a fungal agent (T3). Soil chemical properties, soil aggregate composition, flower-bud biomass, and chlorogenic-acid-related compounds were measured. T1 and T3 increased soil available phosphorus and pH at the pre-flowering stage and increased the proportion of water-stable macroaggregates (>5 mm). Both treatments also increased fresh and dry biomass. T1 showed the highest numerical chlorogenic acid content, whereas T3 was more favourable for the accumulation of isochlorogenic acids A and C. Across plot-level observations, available phosphorus was positively correlated with fresh weight (r = 0.804) and dry weight (r = 0.781), and pH was positively correlated with chlorogenic acid (r = 0.687). Univariate regression and redundancy analysis further indicated that available phosphorus and pH were the soil factors most closely associated with biomass and chlorogenic acid accumulation. These findings provide preliminary field indications that microbial fertilizers may improve yield and medicinal quality in acidic-soil L. macranthoides production. However, the single-season, single-site nature of the experiment warrants cautious interpretation and further validation across broader conditions. The observed associations are consistent with, but do not prove, a mechanistic pathway involving microbe-mediated phosphorus transformation and acidity regulation. Full article

Background/Objectives: Pancreatic ductal adenocarcinoma (PDAC) is characterized by aggressive tumor biology and profound host vulnerability, including pancreatic exocrine insufficiency (PEI), maldigestion, malnutrition, cachexia, sarcopenia, frailty, systemic inflammation, and poor tolerance to multimodal therapy. Gut and intratumoral microbiota have been implicated in pancreatic carcinogenesis, tumor immunity, chemotherapy response, and postoperative outcomes. However, the clinical readiness of microbiome-informed supportive care in PDAC remains uncertain. Results: Current evidence supports plausible mechanistic links among PEI, maldigestion, dysbiosis, microbial metabolites, barrier dysfunction, systemic inflammation, cachexia, sarcopenia, and treatment intolerance. Nevertheless, PDAC microbiome research is limited by major heterogeneity in sampling sites, sequencing platforms, antibiotic exposure, biliary drainage, diet, treatment timing, tumor stage, and analytic pipelines. Evidence is also discordant, particularly regarding alpha diversity and reproducible microbial signatures. Low-biomass tissue contamination and incomplete consideration of fungal and multi-kingdom microbiota further limit interpretation. Conclusions: Microbiome disturbance should currently be viewed as an investigational modifier of nutritional vulnerability and treatment tolerance rather than as a validated clinical biomarker or therapeutic target in PDAC. A clinically responsible framework should distinguish what is actionable now—nutrition screening, PEI management, inflammation and frailty assessment, body-composition evaluation, and treatment-exposure monitoring—from what remains investigational, including microbiome profiling, microbial signatures, probiotics, prebiotics, fecal microbiota transplantation, and metabolite-guided intervention. Full article

Frequent outbreaks of bacterial and fungal diseases in aquaculture cause severe economic losses, making biological control using probiotics a crucial strategy. Bacillus velezensis synthesizes diverse antimicrobial secondary metabolites; however, its biocontrol potential is tightly regulated by environmental signals such as cultivation time. In this study, we investigated the effect of growing time on the antifungal activity of B. velezensis GHZJ-1, isolated from an aquatic environment. It was found that GHZJ-1 shows obvious antifungal activity against the aquatic pathogen Metschnikowia bicuspidata upon 48 h growth but no such activity for 24 h via the agar-diffusion method. We further compared the transcriptomes of GHZJ-1 cells collected at 24 h and 48 h through RNA-Seq. Our results revealed that compared with 24 h, 1821 genes were differentially expressed at 48 h, with 903 upregulated and 918 downregulated. Downregulated genes were enriched in primary metabolic pathways (e.g., ribosome assembly and carbon metabolism), whereas upregulated genes were enriched in secondary metabolite biosynthesis and transmembrane transport. Importantly, 35 upregulated genes directly associated with antimicrobial activity were identified, notably including the ones encoding core elements of a large polyketide synthase (e.g., pksN, log₂FC = 2.24), the petrobactin siderophore system (highest log₂FC = 3.39), and various antimicrobial peptide export systems. Furthermore, the degU gene was activated at 48 h. These data suggest that facing continuously increased environmental stress over time, GHZJ-1 undergoes global transcriptional reprogramming and resource reallocation, downregulating basal metabolism to construct a synergistic antagonistic system coupling chemical defense with nutritional competition. This study elucidates the time-dependent mechanism for antifungal activity in GHZJ-1, providing a molecular theoretical basis for its green biocontrol application in aquaculture diseases caused by fungi. Full article

Immune checkpoint inhibitors have improved outcomes in esophageal cancer across settings, yet clinical benefit remains heterogeneous, with current host-derived biomarkers incompletely predicting response. This mini review evaluates recent studies that integrate gut or intratumoral microbial features with host immune, molecular, or metabolic assessment in esophageal cancer. We classify the evidence using a four-level hierarchy of host-microbiome integration: ecological association, functional association, mechanistic integration, and clinical predictive integration. Tissue studies reveal compartment-specific relationships between microbial diversity or individual taxa and immune architecture, whereas treatment cohorts identify bacterial and fungal signatures associated with pathological or immunotherapy response. Mechanistic studies offer the strongest biological evidence, most notably the Lactobacillus salivarius-indole-3-lactic acid-AhR/NF-κB axis, which drives CD8-positive T-cell exhaustion and resistance to anti-PD-1 therapy. However, biological integration is substantially more advanced than clinical response prediction. Small cohorts, heterogeneous regimens, contamination of low-biomass samples, coarse taxonomic (rather than functional) resolution, confounding by histology, multi-omic layers measured in different patients, and lack of external validation currently jeopardize integration of microbiome to guide treatment. Future studies should use longitudinal, multicenter, compartment-matched sampling and test whether microbial genes or metabolites improve patient selection and predict clinical response beyond established clinical and host biomarkers. Full article

Gastrodia elata, a medicinal and edible plant of the Orchidaceae family, has a long history of medicinal application and extensive development value in China. Endophytes permanently colonize G. elata and form a stable long-term symbiotic relationship with the host. The secondary metabolites produced by these fungi possess diverse structures and multiple biological activities, which are important sources for discovering novel bioactive ingredients that provide natural materials for screening and developing medicinal compounds. This article reviewed the research and development progress of endophytes associated with G. elata, including endophytes’ sources, biological functions, compound classification and pharmacological activities. The results showed that more than 296 secondary metabolites were reported—mainly terpenoids, polyketides, alkaloids, anthraquinones, phenolics—with prominently characterized antifeedant and antibacterial activities. Our work aims to provide scientific references for the in-depth exploration and efficient utilization of G. elata endophytic fungal resources. Full article

Demand for natural red colorants has increased due to regulatory and consumer pressure to replace synthetic additives; however, their industrial application remains limited by challenges related to production, stability, and safety. In this study, the production, physicochemical stability, antimicrobial activity, and preliminary cytotoxicity of an azaphilone-type red colorant produced by Talaromyces sp. C1I3 under submerged fermentation were evaluated. Two sequential Box–Behnken designs identified optimal production conditions at approximately pH 5.8, 60 rpm, and 15.15 g·L⁻¹ monosodium glutamate. Under these conditions, colorant production increased from 1.46 AU_500nm on day 5 to 9.9 AU_500nm on day 10, with estimated kinetic parameters of µmax 0.0109 h⁻¹ and Yx/s 0.63 g·g⁻¹. The colorant showed high thermal stability, retaining approximately 95% of its color after heating at 80 °C for 10 min, and remained stable over a broad pH range, with only 18% degradation after 168 h of light exposure. No significant antimicrobial activity was detected, indicating that the colorant primarily functions as a color additive without additional bioactive effects. Furthermore, no acute cytotoxicity was observed in human neonatal dermal fibroblasts at concentrations ranging from 0.5 to 15 µg·mL⁻¹. These findings demonstrate the potential of this fungal colorant as a stable and safe natural colorant for future industrial applications. Full article

Soil microorganisms are essential for nutrient cycling, plant productivity, and soil health, yet the relative importance of land-use and soil depth in shaping agricultural microbiomes remains poorly understood. This study investigated soil microbial communities across uncultivated land, alfalfa fields, crop systems (feed corn and sweet corn), and orchard systems (walnut and quince) in the Hajdúnánás region of Hungary using shotgun metagenomic sequencing and soil physicochemical analyses. Microbial alpha diversity showed limited variation among land-use systems but declined significantly with soil depth in both bacterial (Kruskal–Wallis, p = 0.00054) and fungal (p = 0.00051) communities. Beta diversity analyses identified soil depth as the primary driver of microbial community composition in both bacterial (R² = 0.305, p = 0.001) and fungal (R² = 0.277, p = 0.001) communities. In contrast, land-use significantly influenced only fungal community composition (R² = 0.250, p = 0.005). Fungal alpha diversity showed significant negative relationships with soil pH and CaCO₃, whereas bacterial diversity exhibited only weak correlations. Crop soils contained the highest numbers of unique bacterial and fungal taxa. Functional analyses revealed significant differences in nutrient cycling, plant-growth-related, decomposition, and environmental adaptation functions among land-use systems. In crop soils, topsoil communities were enriched in oxidative stress-related pathways involved in reactive oxygen species detoxification (ROS), redox homeostasis, and stress regulation, whereas subsoil communities showed a greater representation of antioxidant metabolite production functions. Co-occurrence network analyses indicated greater connectivity in perennial systems, particularly alfalfa soils. Analyses of bacterial and fungal species with reported phytopathogenic potential identified stable cores of phytopathogenic species across agricultural systems, with soil pH emerging as the strongest environmental factor associated with the abundance of phytopathogenic species. Overall, soil depth was the primary driver of bacterial and fungal community assembly, whereas land-use primarily shaped fungal community composition and influenced ecological functions, microbial interaction networks, and the distribution of phytopathogenic species. Full article

Grape white rot, a fungal disease caused by Coniella diplodiella, leads to the decay and abscission of leaves and fruits. This disease is recognized as one of the major fungal diseases affecting the grape industry, significantly impacting the quality and yield of grapes. In this study, a seed-derived Streptomyces strain with high biocontrol activity, designated YTU-S40, was isolated from the seeds of Cnidium monnieri (L.). Molecular phylogenetic identification revealed that this isolate belongs to Streptomyces pseudogriseolus. In vitro plate confrontation experiments demonstrated that YTU-S40 exhibited a robust inhibition rate of 76.2% against C. diplodiella. Furthermore, this strain exhibited relatively broad-spectrum antifungal activity, and genomic analysis predicted that its genome harbors 21 biosynthetic gene clusters responsible for secondary metabolite production. In vivo postharvest grape biocontrol assays verified that YTU-S40 significantly reduced the incidence of grape white rot from 94.4% to 1.9%. Untargeted metabolomic profiling suggested that YTU-S40 may produce bioactive antifungal compounds such as antimycins. Collectively, these findings suggest that YTU-S40 holds considerable promise for development as a biocontrol agent. Full article

Mianning ham is a traditional dry-cured ham from southwestern China, but the coordinated relationships among quality changes, microbial succession, and nonvolatile metabolite remodeling during long-term ripening remain poorly understood. Therefore, samples of Mianning ham aged for one, two, three, and four years were comparatively analyzed. High-throughput sequencing was used to characterize microbial community composition, and untargeted metabolomics was applied to analyze differential metabolite changes and their associations with dominant microorganisms. The results showed that the physicochemical and sensory characteristics of Mianning ham exhibited stage-dependent changes during ripening, with moisture content and pH generally decreasing, while color, texture, and mature flavor characteristics gradually developed. Multivariate statistical analysis identified 99 differential metabolites, which were mainly involved in peptide accumulation, amino acid metabolism, and nitrogen-containing compound transformation. The bacterial communities were mainly composed of Bacillota and Pseudomonadota, while Ascomycota was the predominant fungal phylum. Distinct successional patterns of dominant microbial taxa were observed at different ripening stages. Furthermore, microorganism–metabolite correlation analysis revealed distinct association patterns between internal and surface samples of the ham. Internal microbial communities were mainly associated with nucleotide-related metabolism- and umami-related characteristics, whereas surface microbial communities were more closely associated with the transformation of protein-derived nitrogen-containing compounds and the accumulation of flavor precursors. This study provides insights into the quality formation patterns of Mianning ham during ripening and offers a theoretical basis for ripening-stage evaluation and quality regulation. Full article

Banana Fusarium wilt, caused by Fusarium oxysporum f. sp. cubense (FOC), poses a major threat to global banana production. Straw submergence combined with rice rotation (SFR) has emerged as a promising disease-management strategy, but its underlying mechanisms remain unclear. Here, we conducted a three-year field experiment to determine how SFR alters soil physicochemical properties, microbial communities, and soil metabolites. SFR sharply decreased soil redox potential (Eh) and shifted nitrogen transformation by increasing ammonium nitrogen (AN) and reducing nitrate nitrogen (NN). Eh and NN were positively correlated with culturable Fusarium spp. counts (r = 0.36, p < 0.01), whereas AN was negatively correlated. SFR also reshaped soil microbial communities, reduced the relative abundance of Fusarium, and enriched several putatively antagonistic microbial taxa. Metabolomic profiling showed that several Fusarium-associated metabolites were downregulated and that differential metabolites were enriched in key KEGG pathways. Network analysis further identified Luteimonas as a potential keystone bacterial genus negatively associated with Fusarium-associated metabolites. Partial least squares path modeling suggested that soil physicochemical changes were linked to Fusarium wilt suppression largely through indirect bacterial–fungal–metabolite pathways. These findings indicate that SFR suppresses banana Fusarium wilt, reducing disease incidence to 16.25% at the vigorous growth stage (versus 100% in SC), an 83.8% relative reduction compared with banana monoculture, through coordinated changes in soil Eh and nitrogen status, microbial community structure, and soil metabolic profiles. Full article

Quinoa leaf spot is an important fungal disease that limits quinoa yield and quality. This study aimed to evaluate the pathogenicity of isolates associated with quinoa leaf spot in Qinghai, China, and to screen multifunctional biocontrol bacteria with potential for further development. Pathogenicity assays conducted on healthy quinoa leaves showed that isolates Alternaria alternata AF15 and A. tenuissima AF18 induced typical leaf spot symptoms. The corresponding fungi were successfully re-isolated from the resulting lesions, confirming the pathogenicity of both isolates. Two highly effective biocontrol bacteria, Serratia liquefaciens CB82 and Bacillus velezensis CB316, were subsequently selected through dual-culture assays. Their maximum inhibition rates against the two fungal pathogens reached 56.00% and 57.00%, respectively. Both biocontrol strains exhibited broad adaptability to different temperatures, pH, and NaCl conditions, produced protease, amylase, and cellulase, and showed phosphate-solubilizing activity. Metabolite extraction and fractionation revealed that the antifungal substances were predominantly enriched in the n-butanol fractions, which caused severe shrinkage, surface roughening, breakage, and deformation of the pathogen hyphae. In addition, both strains exhibited strong biofilm-forming capacity and successfully colonized quinoa leaves. Their culturable populations peaked on day 3 after inoculation, reaching 5.58 × 10⁷ and 6.06 × 10⁷ CFU/mL, respectively. In seed germination pouch assays, the bacterial suspensions promoted quinoa root elongation, whereas the fermentation broths increased seedling biomass accumulation in pot experiments. Overall, this study confirmed the pathogenicity of fungal isolates associated with quinoa leaf spot in Qinghai, China, identified two promising biocontrol bacterial strains, and preliminarily characterized their antifungal substances. These findings provide valuable microbial resources and a research basis for the future development of biological control strategies against quinoa leaf spot. Full article

Plants and their endophytic microbiota form a functional holobiont, wherein host-dependent endophytes (HDEs) are proposed to serve as persistent microbial components associated with host continuity. Using long-term in vitro grapevine plantlets, we investigated HDE redistribution and reassembly across successive agar-based subcultures and during the transition to soil-based cultivation. Results showed that the initial tissue niche (shoot-tip versus root-base) imprinted a persistent compositional signature on HDE communities, with distinct cultivar-dependent effects. Numerous microbial amplicon sequence variants (ASVs) remained shared across agar-based and soil-based habitats, demonstrating high persistence of HDE-associated lineages. Bacterial communities exhibited marked plasticity, with plant-associated bacterial lineages contributing substantially to soil community assembly. Notably, 204 root-enriched bacterial ASVs, comprising 10.8–14.3% of the soil community, were recovered, revealing a robust “Root-Specific Legacy”. Bacterial HDEs showed higher redistribution potential (43.3%), whereas fungal transfer was significantly lower (10.4%). Functional profiling suggested habitat-associated functional patterns, with the anaerobic phenotype enriched in soil and predicted enhancements in membrane transport, nucleotide metabolism, glycan biosynthesis, and biosynthesis of secondary metabolites in roots. Cladosporium and Fusarium remained dominant in the fungal core taxa, and habitat transition altered their predicted trophic profiles. Our findings establish HDEs as a resilient biological reservoir capable of niche-specific expansion, contributing to the ecological reassembly of the plant holobiont. Full article