[Objective] We investigated the characteristics of rhizosphere bacterial communities of healthy and root rot-infected strawberry plants across different plots, as well as their correlations with soil physicochemical properties, aiming to discover and isolate beneficial rhizosphere bacteria with significant inhibitory effects against strawberry root rot pathogens to support disease management. [Methods] We utilized high-throughput sequencing combined with bioinformatics analysis to elucidate the differential characteristics and influencing factors of rhizosphere bacterial communities between healthy and diseased strawberry plants. Then, we employed the dilution plate method and dual culture assay to isolate antagonistic bacteria. Subsequently, we determined the taxonomic status of these beneficial strains by combining morphological observation with multi-gene phylogenetic analysis. [Results] The bacterial community diversity varied across different cultivation bases. Compared with that of healthy plants, the rhizosphere soil samples of diseased strawberry plants from the Xinzhuang and Kangshou bases showed decreased bacterial InvSimpson, Chao1, and Shannon evenness indices (P>0.05). Conversely, the rhizosphere soil samples of diseased strawberry plants from the Taolin base showed increased InvSimpson and Shannon evenness indices (P<0.05). Beta diversity analysis revealed that root rot significantly altered the microbial community structure. The complexity and stability of the rhizosphere bacterial co-occurrence network decreased in the diseased samples. Redundancy analysis indicated that soil total organic carbon, available phosphorus, and total potassium were the primary physicochemical factors shaping the bacterial community structure in strawberry rhizosphere. We isolated two bacterial strains, N2-10 and N2-18, that exhibited significant antagonistic activity from the healthy strawberry rhizosphere. The two strains demonstrated inhibition rates ranging from 55.6% to 62.2% and 54.5% to 66.7%, respectively, against the tested strawberry root rot pathogens. We identified strains N2-10 and N2-18 as Bacillus cereus and Bacillus velezensis, respectively. [Conclusion] We clarify how root rot affects strawberry rhizosphere bacterial communities and identify two beneficial rhizosphere bacterial strains with strong biocontrol potential. These findings provide a theoretical basis and valuable strain resources for elucidating the mechanisms of strawberry root rot and developing microbial-based green control technologies.

Raspberry ketone (RK) is a high-value natural aromatic compound widely used in food, flavors and fragrances, and daily chemical products. Traditional plant extraction methods are constrained by raw material availability and high separation costs, while chemical synthesis suffers from high environmental burden and difficulties in meeting market demand for natural-source products. Biocatalytic synthesis represents the core direction for its green manufacturing. However, existing systems remain limited by bottlenecks such as insufficient enzyme activity and substrate tolerance, poor stability of cofactor regeneration systems, and product titers insufficient for industrial needs. [Objective] To construct an efficient, stable, and scalable biocatalytic synthetic system for RK, overcoming existing technical bottlenecks. [Methods] A flavin-independent ene-reductase from Arabidopsis thaliana, AtQOR, was screened and coupled with formate dehydrogenase from Lactobacillus buchneri, LbFDH, to construct an NADPH self-recycling dual-enzyme cascade system. By optimizing vector copy number and gene expression order, an engineered strain co-expressing both enzymes was constructed, and the optimal strain, Escherichia coli 02, was selected. Key reaction conditions for whole-cell biocatalysis were systematically optimized, and a scale-up experiment was performed in a 1 L fermenter using a fed-batch strategy. The product was quantitatively analyzed and structurally verified using gas chromatography (GC) and nuclear magnetic resonance (NMR) spectroscopy. [Results] The selected AtQOR exhibited a specific activity of 10.35 U/mg in catalyzing the conversion of p-hydroxybenzylidene acetone to RK. Under optimal reaction conditions, E. coli 02 produced 37.88 g/L of raspberry ketone from 40 g/L p‑hydroxybenzylidene acetone in 12 h, with a conversion rate of 93.54%. Using a fed‑batch strategy in a 1 L fermenter, the RK titer reached 54.32 g/L in only 10 h, with a conversion rate of 89.43%, and the product was confirmed to be a high-purity target compound. [Conclusion] The dual-enzyme cascade catalytic system constructed in this study substantially overcomes the existing titer bottleneck in RK biosynthesis, providing an efficient, stable, and scalable technological solution for its industrial green manufacturing.

As a key group of the gut microbiota that helps maintain intestinal homeostasis, probiotics have attracted significant attention in life science and medical research. Akkermansia muciniphila (AKK), a strictly anaerobic Gram-negative bacterium, has swiftly become a central topic in gut microbiota research owing to its unique metabolic properties and considerable probiotic potential. This review systematically summarizes the discovery, physiological characteristics, and isolation methodologies and screening of AKK, while placing a particular emphasis on its role in preventing and managing a spectrum of human and animal diseases (including tumors, neurodegenerative disorders, metabolic syndromes, and inflammatory bowel diseases), thereby offering novel perspectives and potential targets for disease intervention. Furthermore, this review elucidates the core mechanisms underlying the probiotic functions of AKK. Specifically, AKK exerts beneficial effects on host health and therapeutic effects on diseases primarily through three key pathways: modulating intestinal microecological balance and barrier integrity, regulating systemic metabolic processes and immune responses, and mediating intricate crosstalk between the intestine and multiple extra-intestinal systems. To assess the translational efficiency of AKK, we summarize the current application status of its functional-related proteins and preparations in health, analyze clinical application scenarios and potential, and discuss existing bottlenecks and challenges in industrial application. This review provides a comprehensive theoretical reference and directional guidance for future basic research, application development, and industrialization of AKK.

Medicinal plants and microorganisms engage in complex, dynamic interactions that profoundly influence plant growth and development, the biosynthesis of secondary metabolites, resistance to pathogens, and adaptation to environmental stressors. Therefore, elucidating the chemical signaling molecules that mediate these interactions is of fundamental importance. The review systematically summarizes the types and functional mechanisms of chemical signals involved in medicinal plant-microorganism interactions. It highlights the roles of both plant- and microorganism-derived signaling molecules in shaping the rhizosphere microbial community assembly, regulating plant growth, and modulating the accumulation of bioactive secondary metabolites. In addition, we discuss the functional divergence of bidirectional signaling in both symbiotic and competitive interactions. Although many mechanism aspects of these chemical signals remain to be fully elucidated, current knowledge provides a solid framework for understanding their regulatory roles. With a “signal-microbiome-function” framework, it is possible to manipulate plant chemical signaling or screen functional microbial strains to reconstruct beneficial rhizosphere microbiomes. Such strategies hold potential for improving soil-plant-microorganism interactions, promoting plant growth, enhance the accumulation of medicinal compounds, and strengthen resistance to pathogens. Overall, these insights are of considerable significance for improving the quality of Chinese medicinal materials and promoting the sustainable and ecological cultivation of medicinal plants.

[Objective] To address the scarcity of neutral sites in Corynebacterium glutamicum ATCC 13032 caused by high G+C content and short intergenic sequences, we established a computer-aided screening platform to identify and characterize efficient neutral sites suitable for heterologous gene integration, aiming to provide key component support for constructing high-performance cell factories. [Methods] A computational screening platform CgNSFinder was constructed to screen candidate neutral sites by integrating heuristic rules such as genomic annotation, neighborhood characteristics, length, and G+C content. The candidate sites were systematically characterized in terms of integration efficiency, cell adaptability, expression intensity, and stability through reporter gene mKate knock-in experiments. We integrated the amylase gene, lycopene synthesis gene cluster, and key L-lysine synthesis genes into the screened sites to verify their heterologous expression ability and application efficiency. [Results] A total of 96 candidate neutral sites were screened out, from which 24 efficient sites were confirmed by experimental characterization. Among them, 19 sites had an integration efficiency greater than 50%, and 22 sites had a fluorescence expression intensity within the range of 2 400-3 500 a.u. The NS3 site showed the best performance, and the lycopene titer reached 48.4 mg/L after multi-copy integration. The L-lysine-producing strain D301 constructed based on the screened sites achieved a titer of 49.51 g/L, a yield of 14.25 g/g, and a productivity of 1.53 g/(L·h) in a 5-L fermenter. [Conclusion] The established neutral site screening method is efficient and feasible. The screened neutral sites are characterized by high integration efficiency, low host interference, and stable expression. This study provides an important tool for metabolic engineering of C. glutamicum.

[Objective] Ergothioneine (EGT), a sulfur-rich derivative of histidine, is utilized in the food, pharmaceutical, and cosmetic industries. However, large-scale production of EGT faces challenges due to the high costs and inefficiency of conventional chemical synthesis and extraction techniques. This study aims to engineer Saccharomyces cerevisiae to provide a microbial platform for EGT biosynthesis. [Methods] The biosynthetic pathway for EGT was reconstructed in S. cerevisiae by heterologously expressing Egt1 from Neurospora crassa and Egt2 from Claviceps purpurea. To overcome the metabolic bottlenecks related to precursor supply, we optimized the upstream pathways for histidine, cysteine, methionine, and S-adenosylmethionine to enhance the flux toward EGT synthesis. Fermentation performance of the engineered strain was assessed in both shake flasks and a 5-L bioreactor. [Results] The engineered S. cerevisiae strain produced 312.8 mg/L of EGT in shake flask fermentation. In a 5-L bioreactor, the strain achieved the EGT titer of 1 312.2 mg/L after 168 h, with the productivity of 7.8 mg/(L·h). [Conclusion] This study presents a metabolic engineering strategy for producing EGT in S. cerevisiae. The approach not only significantly improves EGT biosynthesis but also serves as a reference for microbial production of other compounds.

Microbial antioxidant functions hold significant application potential in the development of holistic health resources, yet their spatial distribution patterns across continuous ecological gradients remain poorly understood. [Objective] To analyze the diversity and spatial distribution characteristics of antioxidant function-related genes in prokaryotes within the Lasha Mountain watershed. [Methods] A spatially exhaustive nine-grid sampling strategy was employed, with 117 sampling points established across the watershed and its 12 sub-basins. PICRUSt2 was used for functional prediction based on high-throughput sequencing data of the 16S rRNA gene. [Results] A total of 38 genes associated with antioxidant compound synthesis were identified and categorized into 12 functional groups. The diversity and total abundance of antioxidant function-related genes were unevenly distributed within the Lasha Mountain watershed, with the downstream region exhibiting higher gene diversity and abundance. The genes associated with non-enzymatic antioxidant compounds dominated both in functional category richness (7 categories) and abundance (0.005 270-0.007 657), with glutathione and thioredoxin genes exhibiting the highest abundance. The overall abundance variation of individual genes (CV=125.85) primarily originated within sub-basins (CV=77.23). After the antioxidant function-related genes were classified by synthesized compounds, the pattern of variation reversed. [Conclusion] The antioxidant function-related genes of prokaryotes exhibit spatial distribution differences in the watershed, and the downstream area—characterized by multiple coupled stress conditions—is a hotspot for the diversity and total abundance of such genes. This study provides an ecological basis for the targeted screening of high-quality antioxidant strains.

[Objective] To investigate the effects of luxS deletion on the biofilm formation and stress tolerance of Listeria monocytogenes and to elucidate the role of luxS in regulating environmental adaptability of this pathogen. [Methods] With Listeria monocytogenes ATCC 19112 as the parental strain, a luxS-deleted mutant, a complemented strain, and an empty-vector control strain were constructed. Growth curve analysis, environmental stress tolerance assays and biofilm formation assays were performed to comparatively analyze phenotypic differences among the wild-type, mutant, and complemented strains. [Results] Compared with the wild-type strain, the luxS-deleted mutant exhibited reduced adaptability under adverse conditions, including low temperature, high osmotic pressure, oxidative stress, and acid stress. Its biofilm-forming ability decreased after 24 h and 48 h of incubation (P<0.01), accompanied by a reduction in the production of extracellular polymeric substances in the biofilm matrix. Further transcriptional analysis revealed that the expression levels of agrA, agrB, lmo2504, and sigB were downregulated (P<0.05), whereas that of ladR was upregulated (P<0.05) following luxS deletion. Under disinfectant stress, MTT assay showed that the metabolic activity of the luxS-deleted strain was lower than that of the wild-type and complemented strains after 48 h of biofilm cultivation (P<0.05). After 72 h, no significant differences were observed among the strains. [Conclusion] These findings demonstrate that luxS plays a critical role in regulating the environmental adaptability of L. monocytogenes and provide a novel theoretical basis for the development of future control and prevention strategies targeting this pathogen.

The increasing emission of sulfur-containing compounds has become a critical factor restricting ecological and environmental security and the sustainable resource utilization. Biological desulfurization technology, relying on the sulfur metabolic pathways of desulfurization microorganisms, enables the efficient conversion of sulfur-containing pollutants and the recovery of sulfur resources under mild conditions, offering both environmental benefits and economic potential. This review systematically summarized the classification and functional characteristics of desulfurization microorganisms, with emphasis on the 4S pathway, the Kodama pathway, and related metabolic modes of organic sulfur-desulfurizing bacteria, as well as the sulfate reduction and sulfur oxidation mechanisms of inorganic sulfur-desulfurizing bacteria. On this basis, the advances in engineering applications in the fields of industrial gas purification, sludge and wastewater treatment, livestock and poultry manure management, domestic waste and agriculture were summarized, and the key environmental factors and carbon source regulation mechanisms affecting desulfurization efficiency were analyzed. Furthermore, the main bottlenecks currently faced by biological desulfurization technology were summarized from the aspects of strain performance, reaction kinetics, mass transfer enhancement, and process stability, and research directions for system enhancement through functional microbial community construction, reactor optimization, and intelligent regulation were proposed. This review aims to provide theoretical references and technical insights for the deepening of biological desulfurization mechanisms and efficient engineering applications.

[Objective] The gut microbiota plays crucial roles in host energy metabolism, immune regulation, and environmental adaptation. However, seasonal variations in the structure, function, and assembly mechanisms of the gut microbiota in the plateau zokor (Eospalax baileyi) remain poorly understood. [Methods] This study employed Illumina high-throughput sequencing technology to perform 16S rRNA (V3-V4 region) sequencing on 17 gastrointestinal content samples of plateau zokors, thus investigating the effects of season (spring vs. winter) on the diversity, function, and assembly processes of the gut microbiota. [Results] The alpha diversity and richness of the gut microbiota in plateau zokors were higher in spring than in winter (P<0.05), and the gut microbiota structure in winter exhibited extremely significant differences (P<0.001). At the phylum and genus levels, the relative abundance of certain dominant microbial taxa differed between seasons (P<0.05). PICRUSt functional prediction revealed that at Level 1, metabolism was the dominant pathway, with the genetic information processing, environmental information processing, human diseases, and organismal systems pathways being enriched in the spring group compared with the winter group (P<0.05). Further analysis of metabolic pathways at Level 2 indicated that pathways related to carbohydrate metabolism, amino acid metabolism, nucleotide metabolism, lipid metabolism, metabolism of other amino acids, and metabolism of terpenoids and polyketides were higher in spring than in winter (P<0.05). The neutral community model (NCM) showed more extensive dispersal of the gut microbiota among individuals in winter (Nm=228.75) than in spring (Nm=216.68). The normalized stochasticity ratio (NST) was less than 0.5 in the spring group, indicating dominance by deterministic processes, while it was greater than 0.5 in the winter group, suggesting dominance by stochastic processes, with significant differences between groups (P<0.001). Further iCAMP analysis revealed that drift and dispersal limitation were the primary ecological processes governing microbial community assembly in both seasons, and the relative contributions of these ecological processes differed between spring and winter (P<0.001). [Conclusion] Season significantly affects the structure, composition, function, and assembly mechanisms of the gut microbiota in plateau zokors. During winter, plateau zokors may save energy by reducing the metabolic activity and information-processing functions of the gut microbiota. In addition, plateau zokors may adjust taxa abundance of the gut microbiota to cope with environmental changes and maintain intestinal homeostasis. These findings provide important insights into the mechanisms by which wild plateau rodents adapt to high-altitude and cold environments from the gut microbiota.