Search Results (421)

Pseudomonas aeruginosa (P. aeruginosa) is a multidrug-resistant opportunistic pathogen that causes both acute and chronic infections and is known for its ability to form biofilms. In the current study, we applied a hypothesis-generating framework primarily based on integrating four different datasets and applying batch correction. Weighted Gene Co-Expression Network Analysis (WGCNA) was performed in parallel with differential expression analysis using limma. Therefore, we aimed to identify potential biofilm-associated gene candidates. Significant candidate genes were subjected to functional analysis and gene ontology, followed by the construction of a protein–protein interaction network using STRING. The Pseudomonas Genome Database was used to highlight the candidate genes. A total of 271, 687, 533, and 277 significantly up-regulated differentially expressed genes (DEGs), as well as 306, 985, 472, and 312 significantly down-regulated DEGs, resulted from the exploratory analysis. Through WGCNA/limma integration, 223 common significantly up-regulated/positively correlated gene candidates were identified. Functional analysis results showed significant enrichment in virulence-related pathways, such as biofilm formation (PA0083, PA0084, hcp1, hcpC, pilH, pilI, pilJ, vfr, pqsA, pqsB, pqsC, pqsE, PA1657, and PA1658). In addition, other virulence-related pathways, such as quorum sensing, phenazine biosynthesis, the bacterial secretion system, and secondary metabolite biosynthesis, were enriched. In conclusion, our hypothesis-generating integrative analysis identifies candidate genes and potential pathways associated with biofilm formation, virulence, and other processes in P. aeruginosa. In light of this, we point out that all candidate genes presented in this study remain hypothesis-generating. Further validation is recommended, including large-scale in silico analyses and in vitro experimental studies. Full article

This study developed a two-step statistically integrated optimization framework to identify the effects of key fermentation medium components controlling hyaluronic acid (HA) biosynthesis by Streptococcus zooepidemicus. As an initial phase, the Plackett–Burman design was employed to identify the most influential components among yeast extract, casein, peptone, beef extract, MgSO₄·7H₂O, K₂HPO₄, KH₂PO₄, and (NH₄)₂SO₄ by conducting 12 fermentation runs, and 30 g/L of glucose was used as the carbon source. Among the eight ingredients, yeast extract, MgSO₄·7H₂O, and KH₂PO₄ were identified as the most significant factors in enhancing HA production. The following steps were based on the selection of the best carbon and yeast extract sources. Sucrose was selected as the optimal carbon source among glucose and lactose, and Tastone 900-Baker’s yeast extract was selected as the optimal nitrogen source among various yeast extract sources. The final phase of the optimization procedure employed the Box–Behnken design to determine the optimal concentrations of three ingredients: yeast extract (10–30 g/L), MgSO₄·7H₂O (0.2–2.0 g/L), and KH₂PO₄ (1–4 g/L). The results depicted that the optimized media formulation, composed of 30.0 g/L of yeast extract, 1.16 g/L of MgSO₄·7H₂O, and 4.0 g/L of KH₂PO₄, enhanced HA production and biomass OD600 to 545.9 mg/L with 1250–1500 kDa and 2.53 OD600 in a 250 mL shake flask scale, which was around a 10-fold increase in HA production compared with run #10 of Plackett–Burman (57.42 mg/L). This study provided preliminary results for future process conditions optimization, scale-up studies, and techno-economic evaluation. Full article

Paclitaxel (Taxol), a taxane diterpenoid from Taxus species, is a clinically important microtubule-stabilizing anticancer agent widely used in chemotherapy. However, its supply remains limited by precursor scarcity and the molecule’s structural complexity. The biosynthetic pathway from geranylgeranyl diphosphate (GGPP) to paclitaxel is estimated to involve 19 to 23 enzymatic steps. Recent multi-omics approaches have substantially elucidated this pathway, yet key mechanistic questions persist, notably the formation of the oxetane ring. Complete heterologous biosynthesis is further hampered by poor cytochrome P450 (CYP) expression in non-native hosts and insufficient metabolic flux. This review synthesizes advances across four themes: (1) progressive elucidation of the biosynthetic pathway, with emphasis on the CYP-mediated oxygenation cascade and oxetane ring formation; (2) genomic and regulatory insights from Taxus genome assemblies, transcription factor networks, and spatial multi-omics; (3) metabolic engineering in microbial hosts, including Escherichia coli, Saccharomyces cerevisiae, and non-conventional chassis; and (4) plant-based heterologous production platforms. Critical bottlenecks are identified, including unresolved enzymatic steps, CYP functional expression, flux partitioning, and bioprocess scale-up. Strategies to overcome these challenges are discussed. Full article

Temporary immersion systems (TISs) are an advanced biotechnological platform for the large-scale cultivation of medicinal plants and the consistent production of high-value secondary metabolites. In this study, we evaluated three immersion regimes with stand-by periods of 4, 8, or 12 h, each paired with a 15-minute immersion period, to optimise shoot growth and colchicine accumulation in Colchicum autumnale L. and Colchicum bivonae Guss. The 4 h stand-by/15 min immersion regime yielded the highest growth index (C. autumnale: 0.75 ± 0.08; C. bivonae: 1.25 ± 0.03) and maximum colchicine content (C. autumnale: 0.19 ± 0.01 mg/g dry biomass; C. bivonae: 0.25 ± 0.02 mg/g dry biomass). Using gas chromatography-mass spectrometry (GC-MS), detailed metabolic profiling of cultures grown under this optimised regime was performed, resulting in the identification of 46 metabolites, including amino acids, organic acids, sugars, sugar alcohols, phenolic, and fatty acids. Volcano plot analysis revealed 11 upregulated and 5 downregulated metabolites in C. autumnale relative to C. bivonae. Significance analysis of metabolomics (SAM) identified 34 metabolites with statistically significant differences between two species. Hierarchical clustering and partial least squares discriminant analysis (PLS-DA) confirmed clear species separation, with Component 1 explaining 68.8% of the total metabolic variance. Glucose-6-phosphate (VIP = 2.01), citric acid (VIP = 1.85), asparagine (VIP = 1.67), and γ-aminobutyric acid (GABA; VIP = 1.52) were the primary biomarkers differentiating the species. These findings confirm that TISs provide an optimised environment for biomass accumulation and stable alkaloid biosynthesis in the Colchicum genus, with C. bivonae emerging as a promising candidate for biotechnological exploitation. Full article

Escherichia coli Nissle 1917 (EcN) has transformed from a traditional probiotic into a versatile microbial cell factory through innovations in genomic tools and metabolic engineering. This review summarizes recent progress in utilizing EcN for biochemical synthesis. First, the development of genetic editing tools is systematically discussed, highlighting how these methods serve as the foundation for metabolic rewiring. Second, we examine EcN bioproduction capabilities, including its application as in situ Live Biotherapeutic Products (LBPs) for targeted disease interventions and its use in the ex vivo biosynthesis of pharmaceuticals and nutraceuticals. Third, optimization strategies for fermentation processes, focusing on diverse carbon source assimilation and industrial scale-up parameters, demonstrate the potential of this strain for commercial production. Through these advancements, EcN emerges as a practical platform for next-generation biomanufacturing and precision medicine. Full article

Background/Objective: Anoectochilus roxburghii, a high-value medicinal orchid, faces significant challenges in quality standardization during large-scale tissue culture due to a lack of understanding of the underlying molecular mechanisms. This study aimed to compare “Jianlan No.2” plantlets cultured under a conventional tissue culture system (CK) and a sugar-free tissue culture system (TD), to elucidate the phenotypic and molecular basis for quality improvement. Methods: A systematic comparison was conducted. Phenotypic traits of plantlets from both systems were measured. Integrated transcriptomic (RNA sequencing) and untargeted metabolomic analyses were employed to identify the molecular differences at the gene expression and metabolite accumulation levels. Results: TD-grown seedlings exhibited significantly superior growth characteristics, including greater plant height, higher rooting rate, and improved transplant survival. Transcriptomic analysis identified 416 differentially expressed genes (DEGs) (44 upregulated, 372 downregulated in TD), which were significantly enriched in pathways related to cell wall organization, apoplast, and photosynthesis. Sixteen key genes were pinpointed as closely associated with seedling growth and metabolic regulation. Metabolomic profiling revealed 502 differentially accumulated metabolites (DAMs), with significant perturbations primarily in phenylpropanoid biosynthesis and terpenoid metabolism. Conclusions: The sugar-free tissue culture system enhances A. roxburghii seedling quality by coordinately modulating photosynthetic capacity, carbon metabolism, and the biosynthesis of key secondary metabolites. These findings provide a crucial molecular foundation for optimizing tissue culture protocols and advancing the standardized, high-quality cultivation of this valuable medicinal plant. Full article

Rice wine fermentation involves complex biochemical dynamics that challenge traditional empirical control, highlighting the need for precise analytical characterization. This narrative review synthesizes the technological evolution of metabolomics from a descriptive tool to a driver of intelligent biomanufacturing. The progression from first-generation compositional profiling to third-generation strategies integrating high-resolution mass spectrometry, real-time sensing, multi-omics approaches, and artificial intelligence is delineated. This evolution has shifted research focus from static component cataloging to dynamic pathway elucidation, enabling deeper interpretation of flavor biosynthesis, functional metabolite formation, and accumulation of safety-related metabolites. Furthermore, this review critically analyzes how multi-omics integration reveals microbiome-metabolite interactions and provides mechanistic targets for quality regulation. Despite these advances, a gap remains between laboratory-scale analytical capabilities and industrial implementation. Key translational bottlenecks are identified, and a future roadmap toward AI-driven digital twin systems and real-time adaptive control is proposed. This framework positions metabolomics not merely as an analytical technique, but as a key foundation of next-generation smart fermentation strategies. Full article

Algae represent one of the most metabolically diverse and ecologically significant groups of photosynthetic organisms, contributing fundamentally to global biogeochemical cycles while offering major potential for biotechnology applications such as biofuels, nutraceuticals, wastewater remediation, and carbon capture. However, the complexity of algal metabolism, driven by evolutionary diversity, compartmentalized cellular organization, and strong environmental coupling, makes predictive understanding of their physiology challenging. In recent years, systems biology approaches combining omics technologies, genome-scale metabolic models, and data-driven methods have begun to transform algal research from descriptive studies toward predictive frameworks. This review summarizes the current state of algal systems biology, highlighting advances in genomics, transcriptomics, proteomics, and metabolomics that enable mechanistic insights into metabolic regulation and environmental adaptation. We discuss the development, curation, and application of algal GEMs across diverse lineages, emphasizing their role in predicting metabolic flux distributions, nutrient utilization, and lipid biosynthesis. In parallel, machine learning and artificial intelligence approaches have emerged to model algal growth and cultivation performance from large physiological datasets. Finally, we discuss emerging hybrid modeling strategies that integrate mechanistic metabolic networks with data-driven predictions, outlining how these frameworks can enable next-generation predictive algal biotechnology and guide rational design of cultivation and metabolic engineering strategies. Full article

Lilium lancifolium Thunb. is an important economic crop widely cultivated and traded across Asia and has significant pharmacological activity. Despite decades of research on their chemical composition, the spatial distribution patterns of characteristic secondary metabolites within the bulbs remain poorly understood. In this study, we used matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) technology to characterize and spatially visualize multiple metabolites within the bulb for the first time. Additionally, ultra-high-performance liquid chromatography-Orbitrap Exploris mass spectrometry (UHPLC-OE-MS) was used to obtain comprehensive metabolite information from the bulbs. Using spatial metabolomics, we successfully identified nine steroidal saponins, three phenolic acid glycerides, and six other metabolites. Subsequently, we analyzed the spatial distribution of steroidal saponins and phenolic acid glycerides, which are key bioactive components. The analysis revealed that most of the steroidal saponins and phenolic acid glycerides, such as deacylbrownioside and regaloside A, exhibited a similar distribution pattern, mainly being enriched in the outer regions (A2, B2) and basal regions (B1, B2) on an individual scale. Further metabolomic and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses indicated that 11 substances detected in the bulbs, including diosgenin, phenylalanine, and acetyl-CoA, were jointly associated with 39 metabolic pathways, including “phenylpropanoid biosynthesis” and “terpenoid backbone biosynthesis”. Based on the above findings, we propose biosynthetic pathways and accumulation patterns of steroidal saponins and phenolic acid glycerides in bulbs. This study provides a basis for precise resource utilization of L. lancifolium bulbs and a methodology to elucidate the biosynthesis of plant metabolites. Full article

Mycotoxins are one of the biggest threats to global food safety, public health, and economic stability. More than 400 mycotoxins have been found to be secondary metabolites of toxigenic fungi, mostly from the genera Aspergillus, Fusarium, Penicillium, and Alternaria. Aflatoxins (AFs), ochratoxin A (OTA), deoxynivalenol (DON), zearalenone (ZEA), fumonisins (FBs), patulin (PAT), and T-2/HT-2 toxins are the most dangerous to the health of people and animals. Conventional physical and chemical decontamination methods are only partially effective and can reduce food quality, leave toxic residues, or be too expensive for smallholder food systems. Recent studies have shown that the application of lactic acid bacteria (LAB) as a biological detoxification method is a safe, cost-effective, and environmentally friendly option, and has a long history of safe use in fermented foods. Selected strains or taxonomic units have been granted GRAS status by the FDA or QPS (Qualified Presumption of Safety) status by EFSA. However, their use for mycotoxin detoxification still requires strain-level safety assessment and efficacy validation in the intended food matrix. There are several mechanisms by which LAB employ to reduce the bioavailability of mycotoxins in food systems: (i) physical adsorption via cell wall components such as peptidoglycan, teichoic acids, and exopolysaccharides; (ii) enzymatic biotransformation that may produce non-toxic or less-toxic metabolites, though the safety of degradation products requires case-by-case toxicological assessment; (iii) antifungal metabolite production that inhibits fungal growth and mycotoxin biosynthesis; and (iv) competitive exclusion of toxigenic fungi during fermentation. This comprehensive review examines the existing evidence on the detoxification of major food mycotoxins by LAB, with an emphasis on mechanisms, strain-specific efficacy, food-matrix applications, and factors that affect detoxification efficacy. Discussion has also been made of translating in vitro findings to in vivo settings and food-scale applications, alongside regulatory frameworks, current challenges, and future research directions. The review also suggests ways to combine LAB with new technologies, such as encapsulation, genetic engineering, and fermentation optimization, to make food systems safer by synergistically controlling mycotoxins. Full article

Silver nanoparticles (AgNPs) have attracted substantial scientific interest in biomedical research owing to their unique physicochemical characteristics, broad-spectrum antimicrobial activity, plasmonic properties, and therapeutic versatility. Although conventional physicochemical synthesis methods enable controlled NPs fabrication, their dependence on hazardous reagents, elevated energy input, and environmentally detrimental processing conditions has stimulated the development of sustainable biogenic alternatives. Biological synthesis utilizing plants, microorganisms, fungi, algae, and purified biomolecules has emerged as an eco-friendly and bio-compatible strategy for AgNP fabrication, enabling simultaneous reduction, stabilization, and intrinsic biofunctionalization of NPs. However, traditional biogenic synthesis remains constrained by limited mechanistic understanding, poor batch reproducibility, inadequate control over physicochemical properties, and challenges in large-scale manufacturing. Recent advances in bioengineering have transformed this field through the integration of metabolic engineering, synthetic biology, microfluidic-assisted synthesis, artificial intelligence-guided process optimization, and continuous-flow biomanufacturing, collectively enabling precision fabrication of biogenic AgNPs with enhanced uniformity, scalability, and functional tunability. Furthermore, strategic surface engineering and functionalization have expanded the applicability of biogenic AgNPs across targeted anticancer therapy, antimicrobial intervention, wound healing, regenerative medicine, drug delivery, and theranostic imaging. Despite these advancements, critical challenges remain regarding nano–bio interactions, toxicological safety, regulatory compliance, and translational scalability. Unlike conventional reviews focused primarily on green synthesis approaches, this review critically highlights emerging bioengineering paradigms that enable programmable, scalable, and precision-controlled biogenic AgNP fabrication. This review comprehensively examines next-generation paradigms and strategies for AgNPs biosynthesis, elucidates the molecular mechanisms governing their formation, highlights emerging functionalization and biomedical application paradigms, and discusses current translational barriers. Forming biogenic composites of AgNPs and heteroatom doped carbon nanodots needs intense research in near future. Full article

Nitzschia sp., a diatom isolated from Paposo (Antofagasta, northern Chile), was evaluated as a biological solution for removing kaolinite-type clay minerals from recycled process water in large-scale copper mining. Optimization of culture conditions to maximize extracellular polymeric substance (EPS) production revealed that supplementing with 0.1 gL⁻¹ of glucose yielded the highest EPS levels on day 17, reaching 1285 ± 58.9 mgL⁻¹ (control equal to 237.8 ± 34 mgL⁻¹ on day 17). However, maximum dry weight biomass productivity was achieved in the presence of sodium carbonate at a concentration of 1 gL⁻¹ (319 ± 12.5 mgL⁻¹d⁻¹), significantly exceeding the productivity of the control group (242.7 ± 5.4 mgL⁻¹d⁻¹). Notably, low glucose supplementation enhanced EPS synthesis. Application of control-derived EPS of 1 gL⁻¹ rapidly decreased kaolinite initial turbidity from ~2024 FNU to ~354 ± 0.74 FNU within one minute. Even more glucose-derived EPS (1 gL⁻¹) further reduced turbidity to ~22.2 ± 0.1 FNU at 5 min, achieving a flocculation efficiency of ~98.9% after 15 min. Genomic analysis and KEGG annotation identified abundant genes for EPS and carbohydrate metabolism, including numerous glycosyltransferases, glycoside hydrolases, and multiple copies of UDP-glucose 4-epimerase, consistent with strong polysaccharide-biosynthesis capacity. Physicochemical characterization (particle sizing, HPLC, SEM, zeta-potential and FT-IR) showed EPS comprised mainly of rhamnose, fucose, arabinose, xylose and glucose, featuring functional groups (–OH, C=O/COO–, O-acetyl, uronic/guluronic signatures) that interact with kaolinite to promote aggregation. These findings demonstrate that Nitzschia-derived EPS, especially from glucose-supplemented cultures, represent promising sustainable bioflocculants for treating kaolinite-contaminated recycled water in mining operations. Full article

The objective of this study was to examine the impact of using a rotary jet head (RJH) on the biosynthesis of byproducts of yeast metabolism and their role in shaping the flavor and aroma profile of bottom fermentation beer (lager style). The tests were conducted on an industrial scale, with fermentation in 3800 hL fermentation tanks. Experiments were conducted in a minimum of six replicates. The main quality indicators, including ethanol concentration and pH, were analyzed, along with key volatile compounds such as acetaldehyde, esters, higher alcohols, and DMS. Additionally, beer samples—both those fermented using forced mixing and those produced conventionally—were subjected to sensory evaluation. The study found that RJH did not cause changes in either the final ethyl alcohol concentration (6.74% in both samples) or the pH measurement results. The rotary jet head increased synthesis of certain volatile components, such as fusel alcohols by 5% and acetate esters by 14% for ethyl acetate and by almost 12% for isoamyl acetate. On the other hand, a more than threefold (8.23 to 2.54 mg/L) decrease in the undesirable acetaldehyde was observed in samples fermented with forced mixing. The resulting beers exhibited statistically significant differences in chemical composition; however, sensory analysis did not reveal these differences. This finding underscores the efficacy of the rotary jet head in expediting the beer production process without compromising its sensory quality. Full article

Alternate wetting and drying (AWD) is a crucial water-saving irrigation strategy in rice production, yet its regulatory mechanisms during drought–rewatering cycles remain unclear, particularly across recovery stages. Using a polyethylene glycol (PEG-6000) hydroponic system, we analyzed physiological, metabolomic, and transcriptomic responses of Oryza sativa L. ssp. japonica under control, continuous drought, and rewatering treatments. The net photosynthetic rate (P_n) recovered within one day after rewatering, and subsequently exceeded control levels, indicating a photosynthetic compensatory effect. In contrast, instantaneous water-use efficiency (WUE) showed only a transient increase before declining thereafter and remaining lower than under continuous drought, revealing an asynchronous recovery in which carbon assimilation precedes the recovery of transpiration. Metabolomic analysis indicated a shift from drought-induced accumulation to recovery-driven metabolic reprogramming, with coordinated up-regulation of central carbon metabolism and chlorophyll biosynthesis. Decreases in citrate, malate, and glutamate suggested their sustained utilization to support nitrogen assimilation and chlorophyll synthesis. Transcriptomic data further revealed large-scale reprogramming during late recovery, including up-regulation of nitrogen assimilation genes (e.g., NIA, NiR), linking carbon–nitrogen coordination with photosynthetic compensation. Overall, these results demonstrate that stage-specific integration of physiological recovery, metabolic restructuring, and transcriptional regulation underlies AWD-induced efficiency and identify early rewatering as a critical window for optimizing WUE. Full article

Aromatic compounds derived from the shikimate (SHK) pathway constitute a diverse class of high-value molecules with applications in the pharmaceutical, food, cosmetic, and chemical industries. In microbial systems, particularly Escherichia coli, this pathway links central carbon metabolism (CCM) to the biosynthesis of L-tyrosine (L-Tyr), L-phenylalanine (L-Phe), and L-tryptophan (L-Trp), which serve as key precursors for structurally diverse metabolites. Over the past decades, metabolic engineering strategies have focused on increasing precursor availability, relieving feedback inhibition, and eliminating competing pathways. More recently, advances in synthetic biology have enabled dynamic control of metabolic flux through pathway modularization, genome-scale interventions, and regulatory circuit design. In this review, we provide a comprehensive overview of the engineering of E. coli for aromatic compound biosynthesis, highlighting key developments in the optimization of the SHK pathway and its major metabolic nodes chorismate, L-Tyr, L-Phe, and L-Trp. We examine emerging approaches, including CRISPR-based regulation, biosensor-driven dynamic control, membrane engineering, and synthetic microbial consortia. Despite significant progress, challenges related to pathway regulation, cofactor balance, metabolic burden, and product toxicity remain critical bottlenecks. Integrating metabolic engineering with synthetic biology is driving the development of programmable, scalable microbial platforms for the efficient bioproduction of aromatic compounds. Full article