Search Results (3,147)

Gamma (γ)-aminobutyric acid (GABA) is a non-proteinogenic amino acid recognized for its primary function as the main inhibitory neurotransmitter in the mammalian central nervous system and its role as a stress-responsive metabolite in various microorganisms. This review critically examines the biosynthesis of GABA by lactic acid bacteria (LAB) via the glutamate decarboxylase (GAD) system and evaluates its potential applications in food and health sectors. The mechanistic details of the GAD pathway are analyzed, focusing on the integrated roles of gadA/gadB decarboxylases, the gadC antiporter, and pyridoxal−5′-phosphate (PLP) dependency in relation to acid resistance, metabolic flux, and strain variability. Taxonomic and strain-level diversity among GABA-producing LAB is assessed, with emphasis on the highly strain-specific nature of GABA production rather than broad species or genus generalizations. Fermentation optimization parameters (pH, temperature, substrate loading, and cofactor management) and scale-up challenges, including techno-economic feasibility and downstream recovery efficiency, are critically evaluated. Integration of LAB-derived GABA into fermented food matrices is discussed with attention to sensory compromises, stability, regulatory factors, and clean-label considerations. Evidence from clinical and preclinical studies is synthesized to assess the physiological significance of dietary GABA, distinguishing between purified GABA supplementation, GABA-enriched fermented foods, and probiotic effects of live LAB, while addressing the GABA paradox and gut–brain axis interactions. Significant research gaps are identified, including the need for standardized quantification methodologies, multi-omics-guided strain engineering, predictive bioprocess modeling, and rigorously designed human trials in realistic food matrices. This review provides a systems-oriented, critical framework to promote scalable and evidence-based advancement of GABA-enriched functional foods. Full article

Rhizosphere microorganisms play critical roles in biogeochemical processes including carbon cycling; however, their linkages to carbon-cycling functions under distinct mine restoration approaches remain unclear. In this study, we compared natural and artificial vegetation restoration via metagenomic sequencing to characterize rhizosphere microbial communities and carbon-cycling functional genes. Artificial restoration (AR) decreased soil electrical conductivity (EC) and salt content (SC) while increasing total phosphorus and available phosphorus by 12.33% and 16.44%, respectively. AR also elevated the relative abundances of genes responsible for degrading aromatic compounds, lignin and starch, along with genes participating in carbon-fixation pathways. Taxa of the Actinomycetia, Chloroflexi, and Solirubrobacterales served as the primary contributors to genes encoding 2-isopropylmalate synthase, α-glucosidase, malate synthase, and α-mannosidase, as well as carbon-fixation-related genes, including aconitate hydratase (ACO), methylmalonyl-CoA mutase subunit (E5.4.99.2A), pyruvate orthophosphate dikinase (ppdK), and phosphoenolpyruvate carboxylase (ppc). Moreover, the relative abundances of carbon-fixation genes exhibited significant positive correlations with EC, SC, nitrate nitrogen (NO₃⁻-N) and ammonium nitrogen (NH₄⁺-N). Overall, microorganisms in AR soils hold relatively high genetic potential for carbon sequestration and decomposition. Such rhizosphere carbon-cycling functions are jointly shaped by restoration strategies and vegetation community composition, and our findings offer key theoretical support for mine ecological restoration. Full article

Fermented cabbage is a globally popular food, whose distinctive flavor is largely determined by microbial metabolism and interspecies interactions. To understand the roles of Lactiplantibacillus plantarum (formerly Lactobacillus plantarum) and Rhodotorula mucilaginosa in regulating microbial community structure and flavor formation during cabbage fermentation, natural fermented cabbage was compared with that inoculated with L. plantarum, R. mucilaginosa and both strains. The results showed that cabbage inoculated with either strain accelerated fermentation, with the fastest acidification observed in the co-inoculated group. Additionally, cabbage inoculated with R. mucilaginosa exhibited a relatively higher total amino acid content (481.50 ± 7.75 g/kg), and the levels of sweet, bitter, and umami amino acids were significantly higher than in the other groups. At the final fermentation stage, 15 differential odor-active compounds (ROAV ≥ 0.1, VIP ≥ 0.5) were identified, contributing mushroom, floral, fruity, malty, buttery, fatty, citrus, soapy, and green notes. Microbial succession analysis revealed that L. plantarum dominated bacterial community restructuring during fermentation and showed antagonistic relationships with the other lactic acid bacteria, including Lactococcus and Weissella. In contrast, R. mucilaginosa mainly influenced fungal community succession and indirectly modulated flavor formation by regulating the abundance of flavor-associated microorganisms, including Lactiplantibacillus, Lactococcus, Staphylococcus, Debaryomyces, and Candida. Correlation analysis further suggested that L. plantarum functioned as a major flavor-driving microorganism; whereas, R. mucilaginosa acted primarily as a microbial community modulator that enhanced flavor complexity through interspecies interactions. These findings highlight the importance of microbial interactions in shaping the flavor characteristics of fermented cabbage and provide insights for improving fermented vegetable flavor through targeted microbial regulation. Full article

Mangrove microorganisms play a fundamental role in regulating sediment biogeochemical processes, particularly carbon storage and trace element cycling. Although numerous studies have examined microbial roles in individual processes, an integrated understanding of how microbial communities simultaneously regulate carbon storage and trace element dynamics in natural and restored mangrove ecosystems remains limited. This review synthesizes the global status of mangrove microbial research and the influence of microbes on carbon storage, trace element accumulation, and speciation in natural and restored mangrove ecosystems, while identifying emerging research trends and knowledge gaps. Our investigation revealed that research on the influence of microbes on carbon storage in mangrove sediments is increasing globally, with considerably increasing trends after 2017. However, less research has been reported on microbial trace metal interrelations than on carbon storage relationships, suggesting that there is limited focus from researchers on this topic. The available evidence indicates that sulfate reduction, microbial extracellular polymeric substances (EPS), microbial necromass formation, redox-driven biogeochemical coupling, and microbially mediated mineral transformations are the principal mechanisms promoting long-term carbon stabilization in mangrove sediments. Therefore, several studies have also suggested that microbial diversity regulates trace element accumulation and speciation through different pathways, such as redox transformation, bioadsorption, EPS-mediated binding or aggregation, biomineralization, and sulfide precipitation, in mangrove sediment. The principal conceptual contribution of this review is the development of an integrated framework demonstrating that microbial processes act as a central biogeochemical bridge connecting carbon storage and trace element cycling, rather than regulating these functions independently. Finally, we identify critical challenges and research priorities, including functional gene characterization, integrated metal–microbe–plant interactions, multi-omics approaches, long-term monitoring, and global meta-analyses, to improve mechanistic understanding and support evidence-based mangrove restoration and blue carbon management. Full article

Natural bioactive compounds found in plants, agri-food by-products, microorganisms, marine sources, and other sustainable biological resources continue to drive scientific innovation due to their structural diversity and wide spectrum of biological activities, supporting advances in pharmaceuticals, nutraceuticals, functional foods, cosmetics, agriculture, and animal nutrition [...] Full article

Background: Multidrug-resistant and biofilm-forming staphylococci pose a threat to the sustainability of public health, livestock health and the ecosystem. Pathogenic potential with a worsening prognosis of therapy is mainly due to methicillin-resistant Staphylococcus aureus (MRSA) or multidrug-resistant Non-aureus staphylococci and mammaliicocci (NASM). Alternative approaches based on the use of biosynthesized nanoparticles or substances of natural origin appear to be promising solutions to the problem of ineffective suppression of infections caused by pathogenic microorganisms. Methods: The aim of this study was to monitor and compare the biological effects of silver nanoparticles prepared by green synthesis using Lavandula angustifolia and lavender essential oil. In particular, the antibacterial, antibiofilm, and biofilm-eradicating effects against biofilm-forming and multidrug-resistant reference strains and field isolates of staphylococci were monitored. Results: AgNPs inhibited the growth and formation of biofilms of S. aureus strains at a concentration of 0.05 μg/μL, but clinical NASM at 0.025 μg/μL. Sensitivity to Lavender essential oil (LEO) was the same against all tested staphylococcal strains, with an antibacterial MIC of 0.901 μg/μL. The essential oil also had an effect on biofilm formation against all tested strains, but its effect was recorded at a tenfold lower concentration (antibiofilm MIC = 0.0901 μg/μL). No eradication activity was recorded for either tested substance. Their activity against the formed biofilms was not recorded. Conclusions: The results demonstrate promising antibacterial and antibiofilm activities of biosynthesized AgNPs and lavender essential oil under in vitro conditions. These findings support further investigation of these materials as potential alternative antimicrobial approaches, particularly in combination with conventional antimicrobial agents. Full article

Hypersaline soils are poly-extreme terrestrial habitats characterized by high salinity, in some cases heavy-metal contamination, temperature fluctuations, and nutrient limitation. These conditions impose strong selective pressures, and many prokaryotic inhabitants still remain uncultured. Here, we conducted an extensive culturomics study of 549 isolates from the hypersaline soils of the Odiel Saltmarshes Natural Area (Southwest Spain) and compared the results with previously generated shotgun metagenomic datasets from the same environment in order to evaluate taxonomic composition, functional potential, and ecological representativeness. Cultivation across media containing 7.5%, 15%, and 25% (w/v) total salts yielded microorganisms belonging to three major phyla: Pseudomonadota, Bacillota (Bacteria) and Halobacteriota (Archaea). At the genus level, bacterial isolates were dominated by Marinobacter, Halomonas, and Aquibacillus at 7.5% (w/v) salinity, whereas extremely halophilic archaea, including Halorubrum, Halogeometricum, and Haloarcula, were predominantly recovered from media containing 25% (w/v) salts. Among the isolates, 57 strains displayed identity values < 98.65% for 16S rRNA gene sequence comparison, suggesting their putative status as new taxa. Comparison with metagenomic datasets showed that culture-dependent approaches successfully recovered the dominant haloarchaeal groups but missed some abundant bacterial phyla, such as Gemmatimonadota. Conversely, culturomics enabled the isolation of unknown species from the rare biosphere, including representatives of the novel genus Terrihalobacillus, which are typically detected at low abundance in metagenomic datasets. Together, these results demonstrate the complementarity of culturomics and metagenomics and provide an insight into the microbial communities inhabiting the hypersaline soils of the Odiel Saltmarshes. Full article

Traditional fermented sausages are widely consumed in China but often face quality and safety risks due to contamination by spoilage and pathogenic microorganisms during natural fermentation. This study investigated the effect of Litsea cubeba essential oil (LCEO) on the microbial community structure and volatile flavor compounds (VFCs) of fermented sausages using multi-omics approaches, including 16S/ITS amplicon sequencing and HS-SPME-GC-MS. The results showed that LCEO significantly altered the microbial community, increasing the relative abundance of Lactobacillus from 4.65% to 76.22% and Debaryomyces from 11.95% to 22.35%, while reducing Staphylococcus and Aspergillus by 47.01% to 4.55% and 37.28% to 17.09%, respectively. A total of 695 VFCs were identified, with terpenoids and hydrocarbons being the most abundant. A differential analysis revealed that LCEO enhanced the relative content of key aroma-active compounds, including ethyl esters and aldehydes, with odor activity values exceeding 1 for fruity-related compounds such as decanoic acid, ethyl ester and nonanoic acid, methyl ester. Strikingly, the elevated levels of these fruity esters translated into significantly higher sensory scores for odor (p < 0.05) in LCEO-treated sausages, as panelists consistently perceived a pronounced fruity and fresh aroma profile, ultimately leading to a superior overall acceptability compared to the control. A correlation analysis indicated strong positive associations between Lactobacillus, Debaryomyces, and major flavor-contributing esters. In conclusion, LCEO potentially reduces the microbial risks and improves the flavor profile of fermented sausages, making it a promising natural additive for meat fermentation. Full article

Sclareol, a natural diterpene, exhibits diverse physiological activities in plants, microorganisms, and animals. Exogenous application of sclareol to Arabidopsis thaliana leaves induces chlorosis-like symptoms accompanied by a reduction in chlorophyll content. In our previous study, a bioassay-guided fractionation approach was employed to isolate endogenous compounds responsible for this decrease, leading to the identification of campesterol and stigmasterol as active phytosterols. Notably, this approach also indicated the presence of additional active substances in fractions lacking these phytosterols. In the present study, we identified α-pinene, oleic acid, triolein, and pipecolic acid as additional compounds capable of reducing chlorophyll content. Exogenous application of each compound to Arabidopsis leaves resulted in a dose-dependent decline in chlorophyll levels. Furthermore, sclareol treatment increased the endogenous accumulation of these metabolites, along with the expression of genes involved in their biosynthesis. Because phytosterols, terpenoids, lipids, and pipecolic acid have been implicated in plant growth and development, stress responses, and disease resistance, the metabolites identified in this study are likely to contribute not only to sclareol-induced chlorophyll reduction but also to other physiological responses elicited by sclareol. Collectively, these findings suggest that sclareol triggers coordinated metabolic reprogramming in Arabidopsis, leading to the accumulation of multiple bioactive metabolites that mediate diverse physiological processes. Full article

Bee bread is a fermented product derived from bee pollen, whose fermentation improves preservation, nutrient bioavailability, and functional properties. However, the microbial succession driving this process, particularly the role of yeasts, remains poorly understood. This study investigated microbial dynamics during fourteen-day spontaneous fermentation of five fresh bee pollen samples from different geographical origins, mimicking natural bee bread formation. Cultivable yeasts and lactic acid bacteria were monitored by viable cell counts and molecular identification. Physicochemical parameters, nutritional components, bioactivities, and pollen structure were evaluated. A clear microbial succession was observed, with Starmerella sp. dominating the early stages and the osmotolerant yeast Zygosaccharomyces rouxii prevailing during the final phase. Together with Apilactobacillus kunkeei, these microorganisms may constitute a cultivable fermentative core involved in bee bread formation. Fermentation significantly increased protein availability, with increases of up to 18%, reduced pH, promoted bee pollen degradation up to 16%, and enhanced antimicrobial activity against Staphylococcus aureus and Listeria monocytogenes. Understanding of cultivable microbiota dynamics during spontaneous bee pollen fermentation could provide an effective natural strategy to stabilize bee pollen while improving its nutritional and functional properties, laying the foundation for developing controlled industrial fermentations to produce bee bread-like products with consistent quality and health-promoting characteristics. Full article

Coumarins are compounds that are naturally found in various plants and are known for their potential pharmacological characteristics, such as anti-inflammatory, antibacterial, antiparasitic, and anticoagulant activities. Despite the potential pharmacological properties, structural modification of coumarins is important to enhance the biological activity, solubility, bioavailability, and various therapeutic characteristics. Microbial transformation is a promising method to modify coumarins since this method offers regioselective and stereospecific transformation, which is challenging to obtain through chemical synthesis. Various microorganisms, including bacteria and fungi, play an essential role in the microbial transformation of coumarins. These microorganisms employ enzymatic mechanisms involving various enzymes to catalyze several reactions, such as hydroxylation, oxidation, reduction, and demethylation. Among these microbial transformation processes, the demethylation process is a significant mechanism for altering the bioactivity of coumarins by converting methoxy groups into hydroxyl groups. Despite all the advantages, microbial transformation also has limitations such as low substrate specificity, contamination during inoculation, variable enzymatic activity, and challenges to scale up the production of bioactive coumarins. These challenges can be addressed through the optimization of the bioprocess to enhance the efficiency of microbial coumarin metabolism. This review provides a comprehensive overview of the microbial transformation of coumarins, highlighting the role of various microorganisms, enzymatic mechanisms, and the transformation processes. Full article

Ellagic acid (EA) is a food-derived polyphenol with multiple biological activities, but its poor water solubility and aggregation in aqueous systems limit its accessibility to gut microorganisms. In this study, Fucus vesiculosus polysaccharide (FVP) was used as a natural carrier to prepare EA/FVP solid dispersions (SDs) with different mass ratios by solvent-assisted evaporation. Compared with pure EA, the SDs markedly improved the apparent solubility and aqueous dispersion stability of EA. The highest apparent solubility was observed for the EA/FVP 3/1 formulation (0.75 ± 0.03 mg/mL), which was approximately 6.25-fold higher than that of pure EA (0.12 ± 0.01 mg/mL). The improved dispersion behavior was associated with increased apparent viscosity, reduced aggregation, decreased crystallinity and possible non-covalent interactions between EA and the polysaccharide matrix. In vitro fecal fermentation showed that SDs enhanced the production of urolithins, including urolithin M5, urolithin M6, urolithin C, iso-urolithin A and urolithin B, without generating new metabolite types. The EA/FVP 1/3 formulation showed the strongest promotion of urolithin production, with iso-urolithin A reaching 2.36 ± 0.28 μM. 16S rRNA sequencing showed that the enhanced urolithin production was accompanied by shifts in the fecal microbial community. Several bacterial genera positively correlated with urolithin biosynthesis, including Bacteroides_H, Negativicoccus, Parabacteroides_B, Unclassified_Eggerthellaceae and Lactococcus_A, were significantly enriched in the SDs groups. These findings suggest that FVP-based SDs may serve as a potential strategy for improving the apparent solubility, aqueous dispersion and microbial biotransformation of EA. Full article

Salinity poses a major threat to sustainable agriculture and coastal ecosystems, resulting in a substantial loss of plant productivity and biodiversity. Although some coastal grass species exhibit natural adaptation to saline conditions, the physiological mechanisms underlying salt tolerance remain incompletely understood, particularly regarding the contribution of plant-associated microorganisms. In a previous study, a commercial cultivar of red fescue (Festuca rubra ssp. rubra cv. Rafael) was shown to be salt sensitive when grown hydroponically, whereas wild populations of F. rubra commonly occur in coastal salt marshes (possibly ssp. litoralis). We hypothesized that this difference in salt tolerance is partly associated with beneficial fungal plant interactions. To test this hypothesis, we investigated whether inoculation with a fungal isolate designated Fusarium sp. 1 and isolated from F. rubra growing on a salt marsh along the Dutch Wadden Sea coast could improve the salinity tolerance of the commercial cultivar. The results showed that inoculation with Fusarium sp. 1 alleviated the salt-induced growth inhibition. At 100 mM NaCl, shoot and root biomass were partially restored relative to non-inoculated controls, accompanied by a significant increase in the shoot-to-root ratio. To investigate the physiological basis of this response, we applied the Microelectrode Ion Flux Estimation (MIFE) technique to quantify Na⁺ -induced K⁺ efflux in roots. Inoculated plants exhibited improved K⁺ homeostasis, characterized by a reduced instantaneous Na⁺-induced K⁺ efflux and a faster recovery of root fluxes. Moreover, inoculated plants grown at 50 and 100 mM NaCl displayed 333% and 397% greater net K⁺ influx, respectively, compared with non-inoculated controls. Our results indicated that inoculation with Fusarium sp. 1 improves the salinity tolerance of F. rubra, likely through enhanced root K⁺ retention. These findings suggest that commercial F. rubra cultivars remain responsive to beneficial microbial associations and highlight the potential of exploring plant–microbe interactions from naturally salt-adapted environments to improve salinity resilience in grasses and potentially other crops. Full article

Lactococcus lactis is an essential industrial “cell factory” used extensively in food fermentation and biotechnology. However, a critical biological question regarding the regulatory mechanisms of the microorganism’s adaptation process remains unresolved: how does the bacterium transcriptionally coordinate the trade-off between primary metabolism and cell-surface remodeling during environmental stress and competence? To date, a unified, global model of its gene regulatory networks (GRNs) that accounts for this transition remains lacking. To address this fragmentation and eliminate selection bias, we integrated the complete compendium of publicly available transcriptomic datasets for L. lactis deposited in the NCBI database as of the summer of 2025. This exhaustive dataset encompasses a wide range of conditions, including thermal, acid, and phage-induced stress, as well as natural competence, providing the necessary transcriptional variance for robust network inference. We implemented an integrated bioinformatics pipeline using the GENIE3 algorithm to infer a core regulatory network common to all tested conditions, complemented by an ensemble of DeepTFactor, Entraf, and p2TF tools to predict strain-specific potential transcription factors (TFs) for L. lactis. The co-expression network partitioned into 50 functional clusters, notably highlighting putative regulators for a unique WxL operon potentially involved in cell-surface modifications. Furthermore, we proposed candidate regulatory targets for the master competence regulator, ComX, and computationally predicted CpsY as a potential LysR-family regulator of branched-chain amino acid metabolism. These findings provide a transcriptomics-based computational model of L. lactis regulation. By clearly distinguishing between established regulatory pathways and purely computational predictions, we suggest several uncharacterized proteins as putative key nodes in the bacterial response to environmental challenges. While requiring direct experimental validation to establish physical interactions, this computational approach generates high-confidence hypotheses and offers a curated resource of candidates for targeted metabolic engineering. Full article

Drainage solution reuse in soilless strawberry production can reduce nutrient-rich discharge, but adoption requires microbial control, hydraulic reliability, and manageable energy demand. This field study evaluated a photovoltaic (PV) assisted ultraviolet-C (UV-C) treatment loop for substrate derived drainage solution in a 132 m² three-tier natural light greenhouse producing ‘Solhyang’ strawberry in Sokcho-si, Republic of Korea. The system used an 11.25 kWp vertical windbreak-type PV facility and a 650 W treatment loop comprising a 250 W low-pressure mercury UV-C reactor, a 350 W pump, and a 50 W controller. The loop operated for 2.5 h day⁻¹, processed 3.25 m³ day⁻¹ as cumulative reactor throughput, and consumed 1.625 kWh day⁻¹, equal to 4.22% of the measured daily PV alternating current (AC) output (38.5 kWh day⁻¹). The drainage solution had low ultraviolet transmittance at 254 nm (UVT₂₅₄; 25–50%) and moderate turbidity (5–30 NTU), conditions that can attenuate UV radiation and shield microorganisms. Across six post fruit set sampling events, the mean log₁₀ reductions were 1.15 ± 0.09 for culturable molds/fungal propagules and 1.64 ± 0.09 for culturable aerobic bacteria; paired tests on log₁₀ transformed counts were significant (p < 0.001). Total coliform bacteria were not detected after treatment, corresponding to a detection limit-based lower-bound reduction of ≥2.69 ± 0.17 log₁₀. Apparent fluence values were treated as engineering estimates rather than validated delivered dose. The results support UV-C sanitation as a preliminary enabling step for drainage solution reuse, while biodosimetry, untreated circulation controls, multi-stage seasonal sampling, full-season recirculation, and crop response validation remain necessary. Full article